diff --git a/.changeset/bright-bats-fold.md b/.changeset/bright-bats-fold.md
new file mode 100644
index 0000000000..514947525c
--- /dev/null
+++ b/.changeset/bright-bats-fold.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/router-generator': patch
+---
+
+Preserve escaped underscore segments when generating index routes across physical and virtual route trees, including pathless layouts, `physical()` prefixes, and `__virtual.ts` subtrees.
diff --git a/packages/router-generator/src/filesystem/physical/getRouteNodes.ts b/packages/router-generator/src/filesystem/physical/getRouteNodes.ts
index a4f72a8df7..09e7fc6c25 100644
--- a/packages/router-generator/src/filesystem/physical/getRouteNodes.ts
+++ b/packages/router-generator/src/filesystem/physical/getRouteNodes.ts
@@ -128,23 +128,26 @@ export async function getRouteNodes(
         const filePath = replaceBackslash(
           path.join(normalizedDir, node.filePath),
         )
-        const prefixPath = cleanPath(`/${normalizedDir}`)
-        const routePath = cleanPath(`/${normalizedDir}${node.routePath}`)
+        const { routePath: prefixPath, originalRoutePath: originalPrefixPath } =
+          normalizedDir
+            ? determineInitialRoutePath(normalizedDir)
+            : { routePath: '', originalRoutePath: '' }
+        const routePath = cleanPath(`${prefixPath}${node.routePath}`)
 
         node.variableName = routePathToVariable(
-          cleanPath(`/${normalizedDir}/${removeExt(node.filePath)}`),
+          cleanPath(`${prefixPath}/${removeExt(node.filePath)}`),
         )
         node._routePathSegmentMetadata = joinRoutePathSegmentMetadata(
           routePath,
           prefixPath,
-          undefined,
+          createRoutePathSegmentMetadata(prefixPath, originalPrefixPath),
           node._routePathSegmentMetadata,
         )
         node.routePath = routePath
         // Keep originalRoutePath aligned with routePath for escape detection
         if (node.originalRoutePath) {
           node.originalRoutePath = cleanPath(
-            `/${normalizedDir}${node.originalRoutePath}`,
+            `${originalPrefixPath}${node.originalRoutePath}`,
           )
         }
         node.filePath = filePath
@@ -313,10 +316,6 @@ export async function getRouteNodes(
                 routePath = '/'
               }
 
-              if (lastOriginalSegment === updatedLastRouteSegment) {
-                originalRoutePath = '/'
-              }
-
               // For layout routes, don't use '/' fallback - an empty path means
               // "layout for the parent path" which is important for physical() mounts
               // where route.tsx at root should have empty path, not '/'
diff --git a/packages/router-generator/src/filesystem/virtual/getRouteNodes.ts b/packages/router-generator/src/filesystem/virtual/getRouteNodes.ts
index be07a648d7..509b1be321 100644
--- a/packages/router-generator/src/filesystem/virtual/getRouteNodes.ts
+++ b/packages/router-generator/src/filesystem/virtual/getRouteNodes.ts
@@ -152,6 +152,12 @@ export async function getRouteNodesRecursive(
   const children = await Promise.all(
     nodes.map(async (node) => {
       if (node.type === 'physical') {
+        const {
+          routePath: routePathPrefix,
+          originalRoutePath: originalRoutePathPrefix,
+        } = node.pathPrefix
+          ? determineInitialRoutePath(removeLeadingSlash(node.pathPrefix))
+          : { routePath: '', originalRoutePath: '' }
         const { routeNodes, physicalDirectories } = await getRouteNodesPhysical(
           {
             ...tsrConfig,
@@ -166,13 +172,16 @@ export async function getRouteNodesRecursive(
         )
         routeNodes.forEach((subtreeNode) => {
           const pathPrefix = cleanPath(
-            `${parent?.routePath ?? ''}${node.pathPrefix}`,
+            `${parent?.routePath ?? ''}${routePathPrefix}`,
+          )
+          const originalPathPrefix = cleanPath(
+            `${parent?.originalRoutePath ?? parent?.routePath ?? ''}${originalRoutePathPrefix}`,
           )
           const literalPathPrefixSegments =
             createLiteralRoutePathSegmentMetadata(pathPrefix, parent, true)
           const routePath = cleanPath(`${pathPrefix}${subtreeNode.routePath}`)
           subtreeNode.variableName = routePathToVariable(
-            `${node.pathPrefix}/${removeExt(subtreeNode.filePath)}`,
+            `${routePathPrefix}/${removeExt(subtreeNode.filePath)}`,
           )
           subtreeNode._routePathSegmentMetadata = joinRoutePathSegmentMetadata(
             routePath,
@@ -184,7 +193,7 @@ export async function getRouteNodesRecursive(
           // Keep originalRoutePath aligned with routePath for escape detection
           if (subtreeNode.originalRoutePath) {
             subtreeNode.originalRoutePath = cleanPath(
-              `${parent?.originalRoutePath ?? parent?.routePath ?? ''}${node.pathPrefix}${subtreeNode.originalRoutePath}`,
+              `${originalPathPrefix}${subtreeNode.originalRoutePath}`,
             )
           }
           subtreeNode.filePath = `${node.directory}/${subtreeNode.filePath}`
@@ -208,11 +217,16 @@ export async function getRouteNodesRecursive(
         case 'index': {
           const { filePath, variableName, fullPath } = getFile(node.file)
           const routePath = `${parentRoutePath}/`
+          const originalRoutePath = `${parentOriginalRoutePath}/`
           return {
             filePath,
             fullPath,
             variableName,
             routePath,
+            originalRoutePath,
+            _routePathSegmentMetadata: parent?._routePathSegmentMetadata
+              ? [...parent._routePathSegmentMetadata]
+              : undefined,
             _fsRouteType: 'static',
             _virtualParentRoutePath: virtualParentRoutePath,
           } satisfies RouteNode
diff --git a/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routeTree.snapshot.ts b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routeTree.snapshot.ts
index 6877c1ac1d..53a35bf149 100644
--- a/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routeTree.snapshot.ts
+++ b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routeTree.snapshot.ts
@@ -9,18 +9,32 @@
 // Additionally, you should also exclude this file from your linter and/or formatter to prevent it from being checked or modified.
 
 import { Route as rootRouteImport } from './routes/__root'
+import { Route as Char91__rootIndexChar93IndexRouteImport } from './routes/[__root-index]/index'
 import { Route as LayoutRouteImport } from './routes/_layout'
 import { Route as FooRouteImport } from './routes/[_]foo'
 import { Route as Char91__literalChar93RouteImport } from './routes/[__literal]'
 import { Route as _layoutRouteImport } from './routes/__layout'
+import { Route as RootIndexIndexRouteImport } from './routes/[_]root-index/index'
 import { Route as LayoutNestedRouteImport } from './routes/_layout/_nested'
 import { Route as LayoutBarRouteImport } from './routes/_layout/[_]bar'
 import { Route as Layout_nested2RouteImport } from './routes/_layout/__nested2'
 import { Route as LayoutChar91__doubleChar93RouteImport } from './routes/_layout/[__double]'
 import { Route as _layoutQuxRouteImport } from './routes/__layout/[_]qux'
+import { Route as LayoutNestedTrailingIndexRouteImport } from './routes/_layout/nested-trailing[_]/index'
+import { Route as LayoutNestedIndexIndexRouteImport } from './routes/_layout/[_]nested-index/index'
+import { Route as LayoutChar91__doubleIndexChar93IndexRouteImport } from './routes/_layout/[__double-index]/index'
 import { Route as LayoutNestedBazRouteImport } from './routes/_layout/_nested/[_]baz'
+import { Route as LayoutNestedIndexIdRouteImport } from './routes/_layout/[_]nested-index/$id'
 import { Route as Layout_nested2DeepRouteImport } from './routes/_layout/__nested2/[_]deep'
+import { Route as LayoutChar91__doubleIndexChar93IdRouteImport } from './routes/_layout/[__double-index]/$id'
+import { Route as LayoutNestedDeepIndexIndexRouteImport } from './routes/_layout/_nested/[_]deep-index/index'
 
+const Char91__rootIndexChar93IndexRoute =
+  Char91__rootIndexChar93IndexRouteImport.update({
+    id: '/__root-index/',
+    path: '/__root-index/',
+    getParentRoute: () => rootRouteImport,
+  } as any)
 const LayoutRoute = LayoutRouteImport.update({
   id: '/_layout',
   getParentRoute: () => rootRouteImport,
@@ -39,6 +53,11 @@ const _layoutRoute = _layoutRouteImport.update({
   id: '/__layout',
   getParentRoute: () => rootRouteImport,
 } as any)
+const RootIndexIndexRoute = RootIndexIndexRouteImport.update({
+  id: '/_root-index/',
+  path: '/_root-index/',
+  getParentRoute: () => rootRouteImport,
+} as any)
 const LayoutNestedRoute = LayoutNestedRouteImport.update({
   id: '/_nested',
   getParentRoute: () => LayoutRoute,
@@ -63,16 +82,50 @@ const _layoutQuxRoute = _layoutQuxRouteImport.update({
   path: '/_qux',
   getParentRoute: () => _layoutRoute,
 } as any)
+const LayoutNestedTrailingIndexRoute =
+  LayoutNestedTrailingIndexRouteImport.update({
+    id: '/nested-trailing_/',
+    path: '/nested-trailing_/',
+    getParentRoute: () => LayoutRoute,
+  } as any)
+const LayoutNestedIndexIndexRoute = LayoutNestedIndexIndexRouteImport.update({
+  id: '/_nested-index/',
+  path: '/_nested-index/',
+  getParentRoute: () => LayoutRoute,
+} as any)
+const LayoutChar91__doubleIndexChar93IndexRoute =
+  LayoutChar91__doubleIndexChar93IndexRouteImport.update({
+    id: '/__double-index/',
+    path: '/__double-index/',
+    getParentRoute: () => LayoutRoute,
+  } as any)
 const LayoutNestedBazRoute = LayoutNestedBazRouteImport.update({
   id: '/_baz',
   path: '/_baz',
   getParentRoute: () => LayoutNestedRoute,
 } as any)
+const LayoutNestedIndexIdRoute = LayoutNestedIndexIdRouteImport.update({
+  id: '/_nested-index/$id',
+  path: '/_nested-index/$id',
+  getParentRoute: () => LayoutRoute,
+} as any)
 const Layout_nested2DeepRoute = Layout_nested2DeepRouteImport.update({
   id: '/_deep',
   path: '/_deep',
   getParentRoute: () => Layout_nested2Route,
 } as any)
+const LayoutChar91__doubleIndexChar93IdRoute =
+  LayoutChar91__doubleIndexChar93IdRouteImport.update({
+    id: '/__double-index/$id',
+    path: '/__double-index/$id',
+    getParentRoute: () => LayoutRoute,
+  } as any)
+const LayoutNestedDeepIndexIndexRoute =
+  LayoutNestedDeepIndexIndexRouteImport.update({
+    id: '/_deep-index/',
+    path: '/_deep-index/',
+    getParentRoute: () => LayoutNestedRoute,
+  } as any)
 
 export interface FileRoutesByFullPath {
   '/': typeof LayoutNestedRouteWithChildren
@@ -81,8 +134,16 @@ export interface FileRoutesByFullPath {
   '/_qux': typeof _layoutQuxRoute
   '/__double': typeof LayoutChar91__doubleChar93Route
   '/_bar': typeof LayoutBarRoute
+  '/__root-index/': typeof Char91__rootIndexChar93IndexRoute
+  '/_root-index/': typeof RootIndexIndexRoute
+  '/__double-index/$id': typeof LayoutChar91__doubleIndexChar93IdRoute
   '/_deep': typeof Layout_nested2DeepRoute
+  '/_nested-index/$id': typeof LayoutNestedIndexIdRoute
   '/_baz': typeof LayoutNestedBazRoute
+  '/__double-index/': typeof LayoutChar91__doubleIndexChar93IndexRoute
+  '/_nested-index/': typeof LayoutNestedIndexIndexRoute
+  '/nested-trailing_/': typeof LayoutNestedTrailingIndexRoute
+  '/_deep-index/': typeof LayoutNestedDeepIndexIndexRoute
 }
 export interface FileRoutesByTo {
   '/': typeof LayoutNestedRouteWithChildren
@@ -91,8 +152,16 @@ export interface FileRoutesByTo {
   '/_qux': typeof _layoutQuxRoute
   '/__double': typeof LayoutChar91__doubleChar93Route
   '/_bar': typeof LayoutBarRoute
+  '/__root-index': typeof Char91__rootIndexChar93IndexRoute
+  '/_root-index': typeof RootIndexIndexRoute
+  '/__double-index/$id': typeof LayoutChar91__doubleIndexChar93IdRoute
   '/_deep': typeof Layout_nested2DeepRoute
+  '/_nested-index/$id': typeof LayoutNestedIndexIdRoute
   '/_baz': typeof LayoutNestedBazRoute
+  '/__double-index': typeof LayoutChar91__doubleIndexChar93IndexRoute
+  '/_nested-index': typeof LayoutNestedIndexIndexRoute
+  '/nested-trailing_': typeof LayoutNestedTrailingIndexRoute
+  '/_deep-index': typeof LayoutNestedDeepIndexIndexRoute
 }
 export interface FileRoutesById {
   __root__: typeof rootRouteImport
@@ -105,8 +174,16 @@ export interface FileRoutesById {
   '/_layout/__nested2': typeof Layout_nested2RouteWithChildren
   '/_layout/_bar': typeof LayoutBarRoute
   '/_layout/_nested': typeof LayoutNestedRouteWithChildren
+  '/__root-index/': typeof Char91__rootIndexChar93IndexRoute
+  '/_root-index/': typeof RootIndexIndexRoute
+  '/_layout/__double-index/$id': typeof LayoutChar91__doubleIndexChar93IdRoute
   '/_layout/__nested2/_deep': typeof Layout_nested2DeepRoute
+  '/_layout/_nested-index/$id': typeof LayoutNestedIndexIdRoute
   '/_layout/_nested/_baz': typeof LayoutNestedBazRoute
+  '/_layout/__double-index/': typeof LayoutChar91__doubleIndexChar93IndexRoute
+  '/_layout/_nested-index/': typeof LayoutNestedIndexIndexRoute
+  '/_layout/nested-trailing_/': typeof LayoutNestedTrailingIndexRoute
+  '/_layout/_nested/_deep-index/': typeof LayoutNestedDeepIndexIndexRoute
 }
 export interface FileRouteTypes {
   fileRoutesByFullPath: FileRoutesByFullPath
@@ -117,8 +194,16 @@ export interface FileRouteTypes {
     | '/_qux'
     | '/__double'
     | '/_bar'
+    | '/__root-index/'
+    | '/_root-index/'
+    | '/__double-index/$id'
     | '/_deep'
+    | '/_nested-index/$id'
     | '/_baz'
+    | '/__double-index/'
+    | '/_nested-index/'
+    | '/nested-trailing_/'
+    | '/_deep-index/'
   fileRoutesByTo: FileRoutesByTo
   to:
     | '/'
@@ -127,8 +212,16 @@ export interface FileRouteTypes {
     | '/_qux'
     | '/__double'
     | '/_bar'
+    | '/__root-index'
+    | '/_root-index'
+    | '/__double-index/$id'
     | '/_deep'
+    | '/_nested-index/$id'
     | '/_baz'
+    | '/__double-index'
+    | '/_nested-index'
+    | '/nested-trailing_'
+    | '/_deep-index'
   id:
     | '__root__'
     | '/__layout'
@@ -140,8 +233,16 @@ export interface FileRouteTypes {
     | '/_layout/__nested2'
     | '/_layout/_bar'
     | '/_layout/_nested'
+    | '/__root-index/'
+    | '/_root-index/'
+    | '/_layout/__double-index/$id'
     | '/_layout/__nested2/_deep'
+    | '/_layout/_nested-index/$id'
     | '/_layout/_nested/_baz'
+    | '/_layout/__double-index/'
+    | '/_layout/_nested-index/'
+    | '/_layout/nested-trailing_/'
+    | '/_layout/_nested/_deep-index/'
   fileRoutesById: FileRoutesById
 }
 export interface RootRouteChildren {
@@ -149,10 +250,19 @@ export interface RootRouteChildren {
   Char91__literalChar93Route: typeof Char91__literalChar93Route
   FooRoute: typeof FooRoute
   LayoutRoute: typeof LayoutRouteWithChildren
+  Char91__rootIndexChar93IndexRoute: typeof Char91__rootIndexChar93IndexRoute
+  RootIndexIndexRoute: typeof RootIndexIndexRoute
 }
 
 declare module '@tanstack/react-router' {
   interface FileRoutesByPath {
+    '/__root-index/': {
+      id: '/__root-index/'
+      path: '/__root-index'
+      fullPath: '/__root-index/'
+      preLoaderRoute: typeof Char91__rootIndexChar93IndexRouteImport
+      parentRoute: typeof rootRouteImport
+    }
     '/_layout': {
       id: '/_layout'
       path: ''
@@ -181,6 +291,13 @@ declare module '@tanstack/react-router' {
       preLoaderRoute: typeof _layoutRouteImport
       parentRoute: typeof rootRouteImport
     }
+    '/_root-index/': {
+      id: '/_root-index/'
+      path: '/_root-index'
+      fullPath: '/_root-index/'
+      preLoaderRoute: typeof RootIndexIndexRouteImport
+      parentRoute: typeof rootRouteImport
+    }
     '/_layout/_nested': {
       id: '/_layout/_nested'
       path: ''
@@ -216,6 +333,27 @@ declare module '@tanstack/react-router' {
       preLoaderRoute: typeof _layoutQuxRouteImport
       parentRoute: typeof _layoutRoute
     }
+    '/_layout/nested-trailing_/': {
+      id: '/_layout/nested-trailing_/'
+      path: '/nested-trailing_'
+      fullPath: '/nested-trailing_/'
+      preLoaderRoute: typeof LayoutNestedTrailingIndexRouteImport
+      parentRoute: typeof LayoutRoute
+    }
+    '/_layout/_nested-index/': {
+      id: '/_layout/_nested-index/'
+      path: '/_nested-index'
+      fullPath: '/_nested-index/'
+      preLoaderRoute: typeof LayoutNestedIndexIndexRouteImport
+      parentRoute: typeof LayoutRoute
+    }
+    '/_layout/__double-index/': {
+      id: '/_layout/__double-index/'
+      path: '/__double-index'
+      fullPath: '/__double-index/'
+      preLoaderRoute: typeof LayoutChar91__doubleIndexChar93IndexRouteImport
+      parentRoute: typeof LayoutRoute
+    }
     '/_layout/_nested/_baz': {
       id: '/_layout/_nested/_baz'
       path: '/_baz'
@@ -223,6 +361,13 @@ declare module '@tanstack/react-router' {
       preLoaderRoute: typeof LayoutNestedBazRouteImport
       parentRoute: typeof LayoutNestedRoute
     }
+    '/_layout/_nested-index/$id': {
+      id: '/_layout/_nested-index/$id'
+      path: '/_nested-index/$id'
+      fullPath: '/_nested-index/$id'
+      preLoaderRoute: typeof LayoutNestedIndexIdRouteImport
+      parentRoute: typeof LayoutRoute
+    }
     '/_layout/__nested2/_deep': {
       id: '/_layout/__nested2/_deep'
       path: '/_deep'
@@ -230,6 +375,20 @@ declare module '@tanstack/react-router' {
       preLoaderRoute: typeof Layout_nested2DeepRouteImport
       parentRoute: typeof Layout_nested2Route
     }
+    '/_layout/__double-index/$id': {
+      id: '/_layout/__double-index/$id'
+      path: '/__double-index/$id'
+      fullPath: '/__double-index/$id'
+      preLoaderRoute: typeof LayoutChar91__doubleIndexChar93IdRouteImport
+      parentRoute: typeof LayoutRoute
+    }
+    '/_layout/_nested/_deep-index/': {
+      id: '/_layout/_nested/_deep-index/'
+      path: '/_deep-index'
+      fullPath: '/_deep-index/'
+      preLoaderRoute: typeof LayoutNestedDeepIndexIndexRouteImport
+      parentRoute: typeof LayoutNestedRoute
+    }
   }
 }
 
@@ -258,10 +417,12 @@ const Layout_nested2RouteWithChildren = Layout_nested2Route._addFileChildren(
 
 interface LayoutNestedRouteChildren {
   LayoutNestedBazRoute: typeof LayoutNestedBazRoute
+  LayoutNestedDeepIndexIndexRoute: typeof LayoutNestedDeepIndexIndexRoute
 }
 
 const LayoutNestedRouteChildren: LayoutNestedRouteChildren = {
   LayoutNestedBazRoute: LayoutNestedBazRoute,
+  LayoutNestedDeepIndexIndexRoute: LayoutNestedDeepIndexIndexRoute,
 }
 
 const LayoutNestedRouteWithChildren = LayoutNestedRoute._addFileChildren(
@@ -273,6 +434,11 @@ interface LayoutRouteChildren {
   Layout_nested2Route: typeof Layout_nested2RouteWithChildren
   LayoutBarRoute: typeof LayoutBarRoute
   LayoutNestedRoute: typeof LayoutNestedRouteWithChildren
+  LayoutChar91__doubleIndexChar93IdRoute: typeof LayoutChar91__doubleIndexChar93IdRoute
+  LayoutNestedIndexIdRoute: typeof LayoutNestedIndexIdRoute
+  LayoutChar91__doubleIndexChar93IndexRoute: typeof LayoutChar91__doubleIndexChar93IndexRoute
+  LayoutNestedIndexIndexRoute: typeof LayoutNestedIndexIndexRoute
+  LayoutNestedTrailingIndexRoute: typeof LayoutNestedTrailingIndexRoute
 }
 
 const LayoutRouteChildren: LayoutRouteChildren = {
@@ -280,6 +446,13 @@ const LayoutRouteChildren: LayoutRouteChildren = {
   Layout_nested2Route: Layout_nested2RouteWithChildren,
   LayoutBarRoute: LayoutBarRoute,
   LayoutNestedRoute: LayoutNestedRouteWithChildren,
+  LayoutChar91__doubleIndexChar93IdRoute:
+    LayoutChar91__doubleIndexChar93IdRoute,
+  LayoutNestedIndexIdRoute: LayoutNestedIndexIdRoute,
+  LayoutChar91__doubleIndexChar93IndexRoute:
+    LayoutChar91__doubleIndexChar93IndexRoute,
+  LayoutNestedIndexIndexRoute: LayoutNestedIndexIndexRoute,
+  LayoutNestedTrailingIndexRoute: LayoutNestedTrailingIndexRoute,
 }
 
 const LayoutRouteWithChildren =
@@ -290,6 +463,8 @@ const rootRouteChildren: RootRouteChildren = {
   Char91__literalChar93Route: Char91__literalChar93Route,
   FooRoute: FooRoute,
   LayoutRoute: LayoutRouteWithChildren,
+  Char91__rootIndexChar93IndexRoute: Char91__rootIndexChar93IndexRoute,
+  RootIndexIndexRoute: RootIndexIndexRoute,
 }
 export const routeTree = rootRouteImport
   ._addFileChildren(rootRouteChildren)
diff --git a/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/[_]root-index/index.tsx b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/[_]root-index/index.tsx
new file mode 100644
index 0000000000..39387c7250
--- /dev/null
+++ b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/[_]root-index/index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_root-index/')({
+  component: () => 'Root Index',
+})
diff --git a/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/[__root-index]/index.tsx b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/[__root-index]/index.tsx
new file mode 100644
index 0000000000..9945c7d300
--- /dev/null
+++ b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/[__root-index]/index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/__root-index/')({
+  component: () => 'Double Root Index',
+})
diff --git a/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/[_]nested-index/$id.tsx b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/[_]nested-index/$id.tsx
new file mode 100644
index 0000000000..e09396020b
--- /dev/null
+++ b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/[_]nested-index/$id.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/_nested-index/$id')({
+  component: () => 'Nested Id',
+})
diff --git a/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/[_]nested-index/index.tsx b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/[_]nested-index/index.tsx
new file mode 100644
index 0000000000..a5f8f95497
--- /dev/null
+++ b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/[_]nested-index/index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/_nested-index/')({
+  component: () => 'Nested Index',
+})
diff --git a/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/[__double-index]/$id.tsx b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/[__double-index]/$id.tsx
new file mode 100644
index 0000000000..2a31adf60c
--- /dev/null
+++ b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/[__double-index]/$id.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/__double-index/$id')({
+  component: () => 'Double Id',
+})
diff --git a/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/[__double-index]/index.tsx b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/[__double-index]/index.tsx
new file mode 100644
index 0000000000..231e787df0
--- /dev/null
+++ b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/[__double-index]/index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/__double-index/')({
+  component: () => 'Double Index',
+})
diff --git a/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/_nested/[_]deep-index/index.tsx b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/_nested/[_]deep-index/index.tsx
new file mode 100644
index 0000000000..4113450ea1
--- /dev/null
+++ b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/_nested/[_]deep-index/index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/_nested/_deep-index/')({
+  component: () => 'Deep Index',
+})
diff --git a/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/nested-trailing[_]/index.tsx b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/nested-trailing[_]/index.tsx
new file mode 100644
index 0000000000..786604a503
--- /dev/null
+++ b/packages/router-generator/tests/generator/physical-pathless-layout-escaped-underscore/routes/_layout/nested-trailing[_]/index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/nested-trailing_/')({
+  component: () => 'Nested Trailing Index',
+})
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routeTree.snapshot.ts b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routeTree.snapshot.ts
index c708ac47c0..70d06b2004 100644
--- a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routeTree.snapshot.ts
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routeTree.snapshot.ts
@@ -13,11 +13,22 @@ import { Route as layoutRouteImport } from './routes/layout'
 import { Route as fooRouteImport } from './routes/foo'
 import { Route as escapedRouteImport } from './routes/escaped'
 import { Route as doubleRouteImport } from './routes/double'
+import { Route as rootIdRouteImport } from './routes/root-id'
 import { Route as nestedLayoutRouteImport } from './routes/nested-layout'
+import { Route as innerLayoutRouteImport } from './routes/inner-layout'
 import { Route as escapedBarRouteImport } from './routes/escaped-bar'
 import { Route as barRouteImport } from './routes/bar'
 import { Route as doubleBarRouteImport } from './routes/double-bar'
+import { Route as rootIndexRouteImport } from './routes/root-index'
 import { Route as bazRouteImport } from './routes/baz'
+import { Route as nestedIdRouteImport } from './routes/nested-id'
+import { Route as escapedIdRouteImport } from './routes/escaped-id'
+import { Route as doubleIdRouteImport } from './routes/double-id'
+import { Route as trailIndexRouteImport } from './routes/trail-index'
+import { Route as nestedIndexRouteImport } from './routes/nested-index'
+import { Route as escapedIndexRouteImport } from './routes/escaped-index'
+import { Route as doubleIndexRouteImport } from './routes/double-index'
+import { Route as deepIndexRouteImport } from './routes/deep-index'
 
 const layoutRoute = layoutRouteImport.update({
   id: '/_layout',
@@ -38,10 +49,19 @@ const doubleRoute = doubleRouteImport.update({
   path: '/__double',
   getParentRoute: () => rootRouteImport,
 } as any)
+const rootIdRoute = rootIdRouteImport.update({
+  id: '/_root-index/$id',
+  path: '/_root-index/$id',
+  getParentRoute: () => rootRouteImport,
+} as any)
 const nestedLayoutRoute = nestedLayoutRouteImport.update({
   id: '/_nested',
   getParentRoute: () => layoutRoute,
 } as any)
+const innerLayoutRoute = innerLayoutRouteImport.update({
+  id: '/_inner',
+  getParentRoute: () => layoutRoute,
+} as any)
 const escapedBarRoute = escapedBarRouteImport.update({
   id: '/_escaped-bar',
   path: '/_escaped-bar',
@@ -57,31 +77,96 @@ const doubleBarRoute = doubleBarRouteImport.update({
   path: '/__double-bar',
   getParentRoute: () => layoutRoute,
 } as any)
+const rootIndexRoute = rootIndexRouteImport.update({
+  id: '/_root-index/',
+  path: '/_root-index/',
+  getParentRoute: () => rootRouteImport,
+} as any)
 const bazRoute = bazRouteImport.update({
   id: '/_baz',
   path: '/_baz',
   getParentRoute: () => nestedLayoutRoute,
 } as any)
+const nestedIdRoute = nestedIdRouteImport.update({
+  id: '/_nested-index/$id',
+  path: '/_nested-index/$id',
+  getParentRoute: () => layoutRoute,
+} as any)
+const escapedIdRoute = escapedIdRouteImport.update({
+  id: '/_escaped-index/$id',
+  path: '/_escaped-index/$id',
+  getParentRoute: () => layoutRoute,
+} as any)
+const doubleIdRoute = doubleIdRouteImport.update({
+  id: '/__double-index/$id',
+  path: '/__double-index/$id',
+  getParentRoute: () => layoutRoute,
+} as any)
+const trailIndexRoute = trailIndexRouteImport.update({
+  id: '/trail_/',
+  path: '/trail_/',
+  getParentRoute: () => layoutRoute,
+} as any)
+const nestedIndexRoute = nestedIndexRouteImport.update({
+  id: '/_nested-index/',
+  path: '/_nested-index/',
+  getParentRoute: () => layoutRoute,
+} as any)
+const escapedIndexRoute = escapedIndexRouteImport.update({
+  id: '/_escaped-index/',
+  path: '/_escaped-index/',
+  getParentRoute: () => layoutRoute,
+} as any)
+const doubleIndexRoute = doubleIndexRouteImport.update({
+  id: '/__double-index/',
+  path: '/__double-index/',
+  getParentRoute: () => layoutRoute,
+} as any)
+const deepIndexRoute = deepIndexRouteImport.update({
+  id: '/_deep-index/',
+  path: '/_deep-index/',
+  getParentRoute: () => innerLayoutRoute,
+} as any)
 
 export interface FileRoutesByFullPath {
   '/__double': typeof doubleRoute
   '/_escaped': typeof escapedRoute
   '/_foo': typeof fooRoute
   '/': typeof nestedLayoutRouteWithChildren
+  '/_root-index/': typeof rootIndexRoute
   '/__double-bar': typeof doubleBarRoute
   '/_bar': typeof barRoute
   '/_escaped-bar': typeof escapedBarRoute
+  '/_root-index/$id': typeof rootIdRoute
+  '/__double-index/': typeof doubleIndexRoute
+  '/_escaped-index/': typeof escapedIndexRoute
+  '/_nested-index/': typeof nestedIndexRoute
+  '/trail_/': typeof trailIndexRoute
+  '/__double-index/$id': typeof doubleIdRoute
+  '/_escaped-index/$id': typeof escapedIdRoute
+  '/_nested-index/$id': typeof nestedIdRoute
   '/_baz': typeof bazRoute
+  '/_deep-index/': typeof deepIndexRoute
 }
 export interface FileRoutesByTo {
   '/__double': typeof doubleRoute
   '/_escaped': typeof escapedRoute
   '/_foo': typeof fooRoute
   '/': typeof nestedLayoutRouteWithChildren
+  '/_root-index': typeof rootIndexRoute
   '/__double-bar': typeof doubleBarRoute
   '/_bar': typeof barRoute
   '/_escaped-bar': typeof escapedBarRoute
+  '/_root-index/$id': typeof rootIdRoute
+  '/__double-index': typeof doubleIndexRoute
+  '/_escaped-index': typeof escapedIndexRoute
+  '/_nested-index': typeof nestedIndexRoute
+  '/trail_': typeof trailIndexRoute
+  '/__double-index/$id': typeof doubleIdRoute
+  '/_escaped-index/$id': typeof escapedIdRoute
+  '/_nested-index/$id': typeof nestedIdRoute
   '/_baz': typeof bazRoute
+  '/_deep-index': typeof deepIndexRoute
 }
 export interface FileRoutesById {
   __root__: typeof rootRouteImport
@@ -89,11 +174,22 @@ export interface FileRoutesById {
   '/_escaped': typeof escapedRoute
   '/_foo': typeof fooRoute
   '/_layout': typeof layoutRouteWithChildren
+  '/_root-index/': typeof rootIndexRoute
   '/_layout/__double-bar': typeof doubleBarRoute
   '/_layout/_bar': typeof barRoute
   '/_layout/_escaped-bar': typeof escapedBarRoute
+  '/_layout/_inner': typeof innerLayoutRouteWithChildren
   '/_layout/_nested': typeof nestedLayoutRouteWithChildren
+  '/_root-index/$id': typeof rootIdRoute
+  '/_layout/__double-index/': typeof doubleIndexRoute
+  '/_layout/_escaped-index/': typeof escapedIndexRoute
+  '/_layout/_nested-index/': typeof nestedIndexRoute
+  '/_layout/trail_/': typeof trailIndexRoute
+  '/_layout/__double-index/$id': typeof doubleIdRoute
+  '/_layout/_escaped-index/$id': typeof escapedIdRoute
+  '/_layout/_nested-index/$id': typeof nestedIdRoute
   '/_layout/_nested/_baz': typeof bazRoute
+  '/_layout/_inner/_deep-index/': typeof deepIndexRoute
 }
 export interface FileRouteTypes {
   fileRoutesByFullPath: FileRoutesByFullPath
@@ -102,31 +198,62 @@ export interface FileRouteTypes {
     | '/_escaped'
     | '/_foo'
     | '/'
+    | '/_root-index/'
     | '/__double-bar'
     | '/_bar'
     | '/_escaped-bar'
+    | '/_root-index/$id'
+    | '/__double-index/'
+    | '/_escaped-index/'
+    | '/_nested-index/'
+    | '/trail_/'
+    | '/__double-index/$id'
+    | '/_escaped-index/$id'
+    | '/_nested-index/$id'
     | '/_baz'
+    | '/_deep-index/'
   fileRoutesByTo: FileRoutesByTo
   to:
     | '/__double'
     | '/_escaped'
     | '/_foo'
     | '/'
+    | '/_root-index'
     | '/__double-bar'
     | '/_bar'
     | '/_escaped-bar'
+    | '/_root-index/$id'
+    | '/__double-index'
+    | '/_escaped-index'
+    | '/_nested-index'
+    | '/trail_'
+    | '/__double-index/$id'
+    | '/_escaped-index/$id'
+    | '/_nested-index/$id'
     | '/_baz'
+    | '/_deep-index'
   id:
     | '__root__'
     | '/__double'
     | '/_escaped'
     | '/_foo'
     | '/_layout'
+    | '/_root-index/'
     | '/_layout/__double-bar'
     | '/_layout/_bar'
     | '/_layout/_escaped-bar'
+    | '/_layout/_inner'
     | '/_layout/_nested'
+    | '/_root-index/$id'
+    | '/_layout/__double-index/'
+    | '/_layout/_escaped-index/'
+    | '/_layout/_nested-index/'
+    | '/_layout/trail_/'
+    | '/_layout/__double-index/$id'
+    | '/_layout/_escaped-index/$id'
+    | '/_layout/_nested-index/$id'
     | '/_layout/_nested/_baz'
+    | '/_layout/_inner/_deep-index/'
   fileRoutesById: FileRoutesById
 }
 export interface RootRouteChildren {
@@ -134,6 +261,8 @@ export interface RootRouteChildren {
   escapedRoute: typeof escapedRoute
   fooRoute: typeof fooRoute
   layoutRoute: typeof layoutRouteWithChildren
+  rootIndexRoute: typeof rootIndexRoute
+  rootIdRoute: typeof rootIdRoute
 }
 
 declare module '@tanstack/react-router' {
@@ -166,6 +295,13 @@ declare module '@tanstack/react-router' {
       preLoaderRoute: typeof doubleRouteImport
       parentRoute: typeof rootRouteImport
     }
+    '/_root-index/$id': {
+      id: '/_root-index/$id'
+      path: '/_root-index/$id'
+      fullPath: '/_root-index/$id'
+      preLoaderRoute: typeof rootIdRouteImport
+      parentRoute: typeof rootRouteImport
+    }
     '/_layout/_nested': {
       id: '/_layout/_nested'
       path: ''
@@ -173,6 +309,13 @@ declare module '@tanstack/react-router' {
       preLoaderRoute: typeof nestedLayoutRouteImport
       parentRoute: typeof layoutRoute
     }
+    '/_layout/_inner': {
+      id: '/_layout/_inner'
+      path: ''
+      fullPath: '/'
+      preLoaderRoute: typeof innerLayoutRouteImport
+      parentRoute: typeof layoutRoute
+    }
     '/_layout/_escaped-bar': {
       id: '/_layout/_escaped-bar'
       path: '/_escaped-bar'
@@ -194,6 +337,13 @@ declare module '@tanstack/react-router' {
       preLoaderRoute: typeof doubleBarRouteImport
       parentRoute: typeof layoutRoute
     }
+    '/_root-index/': {
+      id: '/_root-index/'
+      path: '/_root-index'
+      fullPath: '/_root-index/'
+      preLoaderRoute: typeof rootIndexRouteImport
+      parentRoute: typeof rootRouteImport
+    }
     '/_layout/_nested/_baz': {
       id: '/_layout/_nested/_baz'
       path: '/_baz'
@@ -201,9 +351,77 @@ declare module '@tanstack/react-router' {
       preLoaderRoute: typeof bazRouteImport
       parentRoute: typeof nestedLayoutRoute
     }
+    '/_layout/_nested-index/$id': {
+      id: '/_layout/_nested-index/$id'
+      path: '/_nested-index/$id'
+      fullPath: '/_nested-index/$id'
+      preLoaderRoute: typeof nestedIdRouteImport
+      parentRoute: typeof layoutRoute
+    }
+    '/_layout/_escaped-index/$id': {
+      id: '/_layout/_escaped-index/$id'
+      path: '/_escaped-index/$id'
+      fullPath: '/_escaped-index/$id'
+      preLoaderRoute: typeof escapedIdRouteImport
+      parentRoute: typeof layoutRoute
+    }
+    '/_layout/__double-index/$id': {
+      id: '/_layout/__double-index/$id'
+      path: '/__double-index/$id'
+      fullPath: '/__double-index/$id'
+      preLoaderRoute: typeof doubleIdRouteImport
+      parentRoute: typeof layoutRoute
+    }
+    '/_layout/trail_/': {
+      id: '/_layout/trail_/'
+      path: '/trail_'
+      fullPath: '/trail_/'
+      preLoaderRoute: typeof trailIndexRouteImport
+      parentRoute: typeof layoutRoute
+    }
+    '/_layout/_nested-index/': {
+      id: '/_layout/_nested-index/'
+      path: '/_nested-index'
+      fullPath: '/_nested-index/'
+      preLoaderRoute: typeof nestedIndexRouteImport
+      parentRoute: typeof layoutRoute
+    }
+    '/_layout/_escaped-index/': {
+      id: '/_layout/_escaped-index/'
+      path: '/_escaped-index'
+      fullPath: '/_escaped-index/'
+      preLoaderRoute: typeof escapedIndexRouteImport
+      parentRoute: typeof layoutRoute
+    }
+    '/_layout/__double-index/': {
+      id: '/_layout/__double-index/'
+      path: '/__double-index'
+      fullPath: '/__double-index/'
+      preLoaderRoute: typeof doubleIndexRouteImport
+      parentRoute: typeof layoutRoute
+    }
+    '/_layout/_inner/_deep-index/': {
+      id: '/_layout/_inner/_deep-index/'
+      path: '/_deep-index'
+      fullPath: '/_deep-index/'
+      preLoaderRoute: typeof deepIndexRouteImport
+      parentRoute: typeof innerLayoutRoute
+    }
   }
 }
 
+interface innerLayoutRouteChildren {
+  deepIndexRoute: typeof deepIndexRoute
+}
+
+const innerLayoutRouteChildren: innerLayoutRouteChildren = {
+  deepIndexRoute: deepIndexRoute,
+}
+
+const innerLayoutRouteWithChildren = innerLayoutRoute._addFileChildren(
+  innerLayoutRouteChildren,
+)
+
 interface nestedLayoutRouteChildren {
   bazRoute: typeof bazRoute
 }
@@ -220,14 +438,30 @@ interface layoutRouteChildren {
   doubleBarRoute: typeof doubleBarRoute
   barRoute: typeof barRoute
   escapedBarRoute: typeof escapedBarRoute
+  innerLayoutRoute: typeof innerLayoutRouteWithChildren
   nestedLayoutRoute: typeof nestedLayoutRouteWithChildren
+  doubleIndexRoute: typeof doubleIndexRoute
+  escapedIndexRoute: typeof escapedIndexRoute
+  nestedIndexRoute: typeof nestedIndexRoute
+  trailIndexRoute: typeof trailIndexRoute
+  doubleIdRoute: typeof doubleIdRoute
+  escapedIdRoute: typeof escapedIdRoute
+  nestedIdRoute: typeof nestedIdRoute
 }
 
 const layoutRouteChildren: layoutRouteChildren = {
   doubleBarRoute: doubleBarRoute,
   barRoute: barRoute,
   escapedBarRoute: escapedBarRoute,
+  innerLayoutRoute: innerLayoutRouteWithChildren,
   nestedLayoutRoute: nestedLayoutRouteWithChildren,
+  doubleIndexRoute: doubleIndexRoute,
+  escapedIndexRoute: escapedIndexRoute,
+  nestedIndexRoute: nestedIndexRoute,
+  trailIndexRoute: trailIndexRoute,
+  doubleIdRoute: doubleIdRoute,
+  escapedIdRoute: escapedIdRoute,
+  nestedIdRoute: nestedIdRoute,
 }
 
 const layoutRouteWithChildren =
@@ -238,6 +472,8 @@ const rootRouteChildren: RootRouteChildren = {
   escapedRoute: escapedRoute,
   fooRoute: fooRoute,
   layoutRoute: layoutRouteWithChildren,
+  rootIndexRoute: rootIndexRoute,
+  rootIdRoute: rootIdRoute,
 }
 export const routeTree = rootRouteImport
   ._addFileChildren(rootRouteChildren)
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes.ts b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes.ts
index 27aac72e77..34ebbc111e 100644
--- a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes.ts
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes.ts
@@ -1,13 +1,30 @@
-import { layout, rootRoute, route } from '@tanstack/virtual-file-routes'
+import { index, layout, rootRoute, route } from '@tanstack/virtual-file-routes'
 
 export const routes = rootRoute('__root.tsx', [
   route('/_foo', 'foo.tsx'),
   route('/[_]escaped', 'escaped.tsx'),
   route('/__double', 'double.tsx'),
+  route('/_root-index', [index('root-index.tsx'), route('$id', 'root-id.tsx')]),
   layout('_layout', 'layout.tsx', [
     route('/_bar', 'bar.tsx'),
     route('/[_]escaped-bar', 'escaped-bar.tsx'),
     route('/__double-bar', 'double-bar.tsx'),
+    route('/_nested-index', [
+      index('nested-index.tsx'),
+      route('$id', 'nested-id.tsx'),
+    ]),
+    route('/[_]escaped-index', [
+      index('escaped-index.tsx'),
+      route('$id', 'escaped-id.tsx'),
+    ]),
+    route('/__double-index', [
+      index('double-index.tsx'),
+      route('$id', 'double-id.tsx'),
+    ]),
+    route('/trail_', [index('trail-index.tsx')]),
     layout('_nested', 'nested-layout.tsx', [route('/_baz', 'baz.tsx')]),
+    layout('_inner', 'inner-layout.tsx', [
+      route('/_deep-index', [index('deep-index.tsx')]),
+    ]),
   ]),
 ])
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/deep-index.tsx b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/deep-index.tsx
new file mode 100644
index 0000000000..1952b00184
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/deep-index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/_inner/_deep-index/')({
+  component: () => 'Deep Index',
+})
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/double-id.tsx b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/double-id.tsx
new file mode 100644
index 0000000000..2a31adf60c
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/double-id.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/__double-index/$id')({
+  component: () => 'Double Id',
+})
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/double-index.tsx b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/double-index.tsx
new file mode 100644
index 0000000000..231e787df0
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/double-index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/__double-index/')({
+  component: () => 'Double Index',
+})
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/escaped-id.tsx b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/escaped-id.tsx
new file mode 100644
index 0000000000..a9fad62448
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/escaped-id.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/_escaped-index/$id')({
+  component: () => 'Escaped Id',
+})
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/escaped-index.tsx b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/escaped-index.tsx
new file mode 100644
index 0000000000..9b81fcbadd
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/escaped-index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/_escaped-index/')({
+  component: () => 'Escaped Index',
+})
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/inner-layout.tsx b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/inner-layout.tsx
new file mode 100644
index 0000000000..5266c32a7c
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/inner-layout.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/_inner')({
+  component: () => 'Inner Layout',
+})
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/nested-id.tsx b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/nested-id.tsx
new file mode 100644
index 0000000000..e09396020b
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/nested-id.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/_nested-index/$id')({
+  component: () => 'Nested Id',
+})
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/nested-index.tsx b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/nested-index.tsx
new file mode 100644
index 0000000000..a5f8f95497
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/nested-index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/_nested-index/')({
+  component: () => 'Nested Index',
+})
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/root-id.tsx b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/root-id.tsx
new file mode 100644
index 0000000000..ec329adfd3
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/root-id.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_root-index/$id')({
+  component: () => 'Root Id',
+})
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/root-index.tsx b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/root-index.tsx
new file mode 100644
index 0000000000..39387c7250
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/root-index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_root-index/')({
+  component: () => 'Root Index',
+})
diff --git a/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/trail-index.tsx b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/trail-index.tsx
new file mode 100644
index 0000000000..7794e8f0b3
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-pathless-layout-escaped-underscore/routes/trail-index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/trail_/')({
+  component: () => 'Trail Index',
+})
diff --git a/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routeTree.snapshot.ts b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routeTree.snapshot.ts
new file mode 100644
index 0000000000..b0fd76d1ef
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routeTree.snapshot.ts
@@ -0,0 +1,104 @@
+/* eslint-disable */
+
+// @ts-nocheck
+
+// noinspection JSUnusedGlobalSymbols
+
+// This file was automatically generated by TanStack Router.
+// You should NOT make any changes in this file as it will be overwritten.
+// Additionally, you should also exclude this file from your linter and/or formatter to prevent it from being checked or modified.
+
+import { Route as rootRouteImport } from './routes/__root'
+import { Route as layoutRouteImport } from './routes/layout'
+import { Route as Char91_Char93nestedIndexRouteImport } from './routes/physical-routes/[_]nested/index'
+import { Route as Char91_Char93nestedIdRouteImport } from './routes/physical-routes/[_]nested/$id'
+
+const layoutRoute = layoutRouteImport.update({
+  id: '/_layout',
+  getParentRoute: () => rootRouteImport,
+} as any)
+const Char91_Char93nestedIndexRoute =
+  Char91_Char93nestedIndexRouteImport.update({
+    id: '/_nested/',
+    path: '/_nested/',
+    getParentRoute: () => layoutRoute,
+  } as any)
+const Char91_Char93nestedIdRoute = Char91_Char93nestedIdRouteImport.update({
+  id: '/_nested/$id',
+  path: '/_nested/$id',
+  getParentRoute: () => layoutRoute,
+} as any)
+
+export interface FileRoutesByFullPath {
+  '/': typeof layoutRouteWithChildren
+  '/_nested/$id': typeof Char91_Char93nestedIdRoute
+  '/_nested/': typeof Char91_Char93nestedIndexRoute
+}
+export interface FileRoutesByTo {
+  '/': typeof layoutRouteWithChildren
+  '/_nested/$id': typeof Char91_Char93nestedIdRoute
+  '/_nested': typeof Char91_Char93nestedIndexRoute
+}
+export interface FileRoutesById {
+  __root__: typeof rootRouteImport
+  '/_layout': typeof layoutRouteWithChildren
+  '/_layout/_nested/$id': typeof Char91_Char93nestedIdRoute
+  '/_layout/_nested/': typeof Char91_Char93nestedIndexRoute
+}
+export interface FileRouteTypes {
+  fileRoutesByFullPath: FileRoutesByFullPath
+  fullPaths: '/' | '/_nested/$id' | '/_nested/'
+  fileRoutesByTo: FileRoutesByTo
+  to: '/' | '/_nested/$id' | '/_nested'
+  id: '__root__' | '/_layout' | '/_layout/_nested/$id' | '/_layout/_nested/'
+  fileRoutesById: FileRoutesById
+}
+export interface RootRouteChildren {
+  layoutRoute: typeof layoutRouteWithChildren
+}
+
+declare module '@tanstack/react-router' {
+  interface FileRoutesByPath {
+    '/_layout': {
+      id: '/_layout'
+      path: ''
+      fullPath: '/'
+      preLoaderRoute: typeof layoutRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+    '/_layout/_nested/': {
+      id: '/_layout/_nested/'
+      path: '/_nested'
+      fullPath: '/_nested/'
+      preLoaderRoute: typeof Char91_Char93nestedIndexRouteImport
+      parentRoute: typeof layoutRoute
+    }
+    '/_layout/_nested/$id': {
+      id: '/_layout/_nested/$id'
+      path: '/_nested/$id'
+      fullPath: '/_nested/$id'
+      preLoaderRoute: typeof Char91_Char93nestedIdRouteImport
+      parentRoute: typeof layoutRoute
+    }
+  }
+}
+
+interface layoutRouteChildren {
+  Char91_Char93nestedIdRoute: typeof Char91_Char93nestedIdRoute
+  Char91_Char93nestedIndexRoute: typeof Char91_Char93nestedIndexRoute
+}
+
+const layoutRouteChildren: layoutRouteChildren = {
+  Char91_Char93nestedIdRoute: Char91_Char93nestedIdRoute,
+  Char91_Char93nestedIndexRoute: Char91_Char93nestedIndexRoute,
+}
+
+const layoutRouteWithChildren =
+  layoutRoute._addFileChildren(layoutRouteChildren)
+
+const rootRouteChildren: RootRouteChildren = {
+  layoutRoute: layoutRouteWithChildren,
+}
+export const routeTree = rootRouteImport
+  ._addFileChildren(rootRouteChildren)
+  ._addFileTypes<FileRouteTypes>()
diff --git a/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes.ts b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes.ts
new file mode 100644
index 0000000000..8cd9a3a353
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes.ts
@@ -0,0 +1,5 @@
+import { layout, physical, rootRoute } from '@tanstack/virtual-file-routes'
+
+export const routes = rootRoute('__root.tsx', [
+  layout('_layout', 'layout.tsx', [physical('', 'physical-routes')]),
+])
diff --git a/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes/__root.tsx b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes/__root.tsx
new file mode 100644
index 0000000000..9c657c7d5b
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes/__root.tsx
@@ -0,0 +1,3 @@
+import { createRootRoute } from '@tanstack/react-router'
+
+export const Route = createRootRoute()
diff --git a/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes/layout.tsx b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes/layout.tsx
new file mode 100644
index 0000000000..9c1673dafd
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes/layout.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout')({
+  component: () => 'Layout',
+})
diff --git a/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes/physical-routes/[_]nested/$id.tsx b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes/physical-routes/[_]nested/$id.tsx
new file mode 100644
index 0000000000..4b06b8799e
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes/physical-routes/[_]nested/$id.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/_nested/$id')({
+  component: () => 'Nested Id',
+})
diff --git a/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes/physical-routes/[_]nested/index.tsx b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes/physical-routes/[_]nested/index.tsx
new file mode 100644
index 0000000000..b8eca0e427
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/routes/physical-routes/[_]nested/index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_layout/_nested/')({
+  component: () => 'Nested Index',
+})
diff --git a/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/tsr.config.json b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/tsr.config.json
new file mode 100644
index 0000000000..4d587108e3
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-pathless-layout-literal-index/tsr.config.json
@@ -0,0 +1,5 @@
+{
+  "routesDirectory": "./routes",
+  "generatedRouteTree": "./routeTree.gen.ts",
+  "virtualRouteConfig": "./routes.ts"
+}
diff --git a/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routeTree.snapshot.ts b/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routeTree.snapshot.ts
new file mode 100644
index 0000000000..63b1df0f40
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routeTree.snapshot.ts
@@ -0,0 +1,77 @@
+/* eslint-disable */
+
+// @ts-nocheck
+
+// noinspection JSUnusedGlobalSymbols
+
+// This file was automatically generated by TanStack Router.
+// You should NOT make any changes in this file as it will be overwritten.
+// Additionally, you should also exclude this file from your linter and/or formatter to prevent it from being checked or modified.
+
+import { Route as rootRouteImport } from './routes/__root'
+import { Route as ApiIndexRouteImport } from './routes/physical-routes/index'
+import { Route as ApiIdRouteImport } from './routes/physical-routes/$id'
+
+const ApiIndexRoute = ApiIndexRouteImport.update({
+  id: '/_api/',
+  path: '/_api/',
+  getParentRoute: () => rootRouteImport,
+} as any)
+const ApiIdRoute = ApiIdRouteImport.update({
+  id: '/_api/$id',
+  path: '/_api/$id',
+  getParentRoute: () => rootRouteImport,
+} as any)
+
+export interface FileRoutesByFullPath {
+  '/_api/$id': typeof ApiIdRoute
+  '/_api/': typeof ApiIndexRoute
+}
+export interface FileRoutesByTo {
+  '/_api/$id': typeof ApiIdRoute
+  '/_api': typeof ApiIndexRoute
+}
+export interface FileRoutesById {
+  __root__: typeof rootRouteImport
+  '/_api/$id': typeof ApiIdRoute
+  '/_api/': typeof ApiIndexRoute
+}
+export interface FileRouteTypes {
+  fileRoutesByFullPath: FileRoutesByFullPath
+  fullPaths: '/_api/$id' | '/_api/'
+  fileRoutesByTo: FileRoutesByTo
+  to: '/_api/$id' | '/_api'
+  id: '__root__' | '/_api/$id' | '/_api/'
+  fileRoutesById: FileRoutesById
+}
+export interface RootRouteChildren {
+  ApiIdRoute: typeof ApiIdRoute
+  ApiIndexRoute: typeof ApiIndexRoute
+}
+
+declare module '@tanstack/react-router' {
+  interface FileRoutesByPath {
+    '/_api/': {
+      id: '/_api/'
+      path: '/_api'
+      fullPath: '/_api/'
+      preLoaderRoute: typeof ApiIndexRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+    '/_api/$id': {
+      id: '/_api/$id'
+      path: '/_api/$id'
+      fullPath: '/_api/$id'
+      preLoaderRoute: typeof ApiIdRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+  }
+}
+
+const rootRouteChildren: RootRouteChildren = {
+  ApiIdRoute: ApiIdRoute,
+  ApiIndexRoute: ApiIndexRoute,
+}
+export const routeTree = rootRouteImport
+  ._addFileChildren(rootRouteChildren)
+  ._addFileTypes<FileRouteTypes>()
diff --git a/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routes.ts b/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routes.ts
new file mode 100644
index 0000000000..8e3883cec6
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routes.ts
@@ -0,0 +1,5 @@
+import { physical, rootRoute } from '@tanstack/virtual-file-routes'
+
+export const routes = rootRoute('__root.tsx', [
+  physical('/[_]api', 'physical-routes'),
+])
diff --git a/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routes/__root.tsx b/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routes/__root.tsx
new file mode 100644
index 0000000000..9c657c7d5b
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routes/__root.tsx
@@ -0,0 +1,3 @@
+import { createRootRoute } from '@tanstack/react-router'
+
+export const Route = createRootRoute()
diff --git a/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routes/physical-routes/$id.tsx b/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routes/physical-routes/$id.tsx
new file mode 100644
index 0000000000..e45ad32d5d
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routes/physical-routes/$id.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_api/$id')({
+  component: () => 'API Id',
+})
diff --git a/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routes/physical-routes/index.tsx b/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routes/physical-routes/index.tsx
new file mode 100644
index 0000000000..ac44aee10d
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/routes/physical-routes/index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_api/')({
+  component: () => 'API Index',
+})
diff --git a/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/tsr.config.json b/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/tsr.config.json
new file mode 100644
index 0000000000..4d587108e3
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-physical-prefix-escaped-underscore/tsr.config.json
@@ -0,0 +1,5 @@
+{
+  "routesDirectory": "./routes",
+  "generatedRouteTree": "./routeTree.gen.ts",
+  "virtualRouteConfig": "./routes.ts"
+}
diff --git a/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routeTree.snapshot.ts b/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routeTree.snapshot.ts
new file mode 100644
index 0000000000..bb8b39ad4a
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routeTree.snapshot.ts
@@ -0,0 +1,77 @@
+/* eslint-disable */
+
+// @ts-nocheck
+
+// noinspection JSUnusedGlobalSymbols
+
+// This file was automatically generated by TanStack Router.
+// You should NOT make any changes in this file as it will be overwritten.
+// Additionally, you should also exclude this file from your linter and/or formatter to prevent it from being checked or modified.
+
+import { Route as rootRouteImport } from './routes/__root'
+import { Route as AreaIndexRouteImport } from './routes/[_]area/index'
+import { Route as AreaChildRouteImport } from './routes/[_]area/child'
+
+const AreaIndexRoute = AreaIndexRouteImport.update({
+  id: '/_area/',
+  path: '/_area/',
+  getParentRoute: () => rootRouteImport,
+} as any)
+const AreaChildRoute = AreaChildRouteImport.update({
+  id: '/_area/child',
+  path: '/_area/child',
+  getParentRoute: () => rootRouteImport,
+} as any)
+
+export interface FileRoutesByFullPath {
+  '/_area/child': typeof AreaChildRoute
+  '/_area/': typeof AreaIndexRoute
+}
+export interface FileRoutesByTo {
+  '/_area/child': typeof AreaChildRoute
+  '/_area': typeof AreaIndexRoute
+}
+export interface FileRoutesById {
+  __root__: typeof rootRouteImport
+  '/_area/child': typeof AreaChildRoute
+  '/_area/': typeof AreaIndexRoute
+}
+export interface FileRouteTypes {
+  fileRoutesByFullPath: FileRoutesByFullPath
+  fullPaths: '/_area/child' | '/_area/'
+  fileRoutesByTo: FileRoutesByTo
+  to: '/_area/child' | '/_area'
+  id: '__root__' | '/_area/child' | '/_area/'
+  fileRoutesById: FileRoutesById
+}
+export interface RootRouteChildren {
+  AreaChildRoute: typeof AreaChildRoute
+  AreaIndexRoute: typeof AreaIndexRoute
+}
+
+declare module '@tanstack/react-router' {
+  interface FileRoutesByPath {
+    '/_area/': {
+      id: '/_area/'
+      path: '/_area'
+      fullPath: '/_area/'
+      preLoaderRoute: typeof AreaIndexRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+    '/_area/child': {
+      id: '/_area/child'
+      path: '/_area/child'
+      fullPath: '/_area/child'
+      preLoaderRoute: typeof AreaChildRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+  }
+}
+
+const rootRouteChildren: RootRouteChildren = {
+  AreaChildRoute: AreaChildRoute,
+  AreaIndexRoute: AreaIndexRoute,
+}
+export const routeTree = rootRouteImport
+  ._addFileChildren(rootRouteChildren)
+  ._addFileTypes<FileRouteTypes>()
diff --git a/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routes/[_]area/__virtual.ts b/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routes/[_]area/__virtual.ts
new file mode 100644
index 0000000000..fd1baf16be
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routes/[_]area/__virtual.ts
@@ -0,0 +1,10 @@
+import {
+  defineVirtualSubtreeConfig,
+  index,
+  route,
+} from '@tanstack/virtual-file-routes'
+
+export default defineVirtualSubtreeConfig([
+  index('index.tsx'),
+  route('/child', 'child.tsx'),
+])
diff --git a/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routes/[_]area/child.tsx b/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routes/[_]area/child.tsx
new file mode 100644
index 0000000000..f3af7057cb
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routes/[_]area/child.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_area/child')({
+  component: () => 'Area Child',
+})
diff --git a/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routes/[_]area/index.tsx b/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routes/[_]area/index.tsx
new file mode 100644
index 0000000000..90b81675e6
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routes/[_]area/index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/_area/')({
+  component: () => 'Area Index',
+})
diff --git a/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routes/__root.tsx b/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routes/__root.tsx
new file mode 100644
index 0000000000..9c657c7d5b
--- /dev/null
+++ b/packages/router-generator/tests/generator/virtual-subtree-in-escaped-physical-directory/routes/__root.tsx
@@ -0,0 +1,3 @@
+import { createRootRoute } from '@tanstack/react-router'
+
+export const Route = createRootRoute()
diff --git a/packages/router-generator/tests/utils.test.ts b/packages/router-generator/tests/utils.test.ts
index 6e1a58a204..0cdce3cfae 100644
--- a/packages/router-generator/tests/utils.test.ts
+++ b/packages/router-generator/tests/utils.test.ts
@@ -2,6 +2,8 @@ import { describe, expect, it, vi } from 'vitest'
 import {
   RoutePrefixMap,
   cleanPath,
+  createLiteralRoutePathSegmentMetadata,
+  createRoutePathSegmentMetadata,
   createRouteNodesByFullPath,
   createRouteNodesByTo,
   determineInitialRoutePath,
@@ -58,6 +60,88 @@ describe('inferFullPath', () => {
 
     expect(inferFullPath(node)).toBe('/__foo')
   })
+
+  it('preserves explicit literal leading underscores on index routes after removing pathless ancestors', () => {
+    const parent = {
+      routePath: '/_layout',
+    } as unknown as RouteNode
+    const node = {
+      routePath: '/_layout/_nested/',
+      originalRoutePath: '/_layout/_nested/',
+      _routePathSegmentMetadata: createLiteralRoutePathSegmentMetadata(
+        '/_layout/_nested',
+        parent,
+        true,
+      ),
+    } as unknown as RouteNode
+
+    expect(inferFullPath(node)).toBe('/_nested/')
+  })
+
+  it('removes pathless index route segments when they are not marked literal', () => {
+    const node = {
+      routePath: '/_layout/_nested/',
+      originalRoutePath: '/_layout/_nested/',
+    } as unknown as RouteNode
+
+    expect(inferFullPath(node)).toBe('/')
+  })
+
+  it('preserves escaped trailing underscores on index routes', () => {
+    const node = {
+      routePath: '/_layout/foo_/',
+      originalRoutePath: '/_layout/foo[_]/',
+      _routePathSegmentMetadata: createRoutePathSegmentMetadata(
+        '/_layout/foo_/',
+        '/_layout/foo[_]/',
+      ),
+    } as unknown as RouteNode
+
+    expect(inferFullPath(node)).toBe('/foo_/')
+  })
+
+  it('removes unescaped trailing underscores on index routes', () => {
+    const node = {
+      routePath: '/_layout/foo_/',
+      originalRoutePath: '/_layout/foo_/',
+    } as unknown as RouteNode
+
+    expect(inferFullPath(node)).toBe('/foo/')
+  })
+})
+
+describe('createRoutePathSegmentMetadata', () => {
+  it('preserves escaped trailing underscores on index routes', () => {
+    const metadata = createRoutePathSegmentMetadata('/foo_/', '/foo[_]/')
+
+    expect(metadata).toHaveLength(3)
+    expect(metadata?.[1]).toEqual({ literalTrailingUnderscore: true })
+  })
+
+  it('preserves mixed escaped leading and trailing underscores', () => {
+    const metadata = createRoutePathSegmentMetadata('/_foo_/', '/[_]foo[_]/')
+
+    expect(metadata).toHaveLength(3)
+    expect(metadata?.[1]).toEqual({
+      literalLeadingUnderscore: true,
+      literalTrailingUnderscore: true,
+    })
+  })
+
+  it('tracks multiple literal underscore segments independently', () => {
+    const metadata = createRoutePathSegmentMetadata(
+      '/_foo/bar_/_baz_/',
+      '/[_]foo/bar[_]/[_baz_]/',
+    )
+
+    expect(metadata).toHaveLength(5)
+    expect(metadata?.[1]).toEqual({ literalLeadingUnderscore: true })
+    expect(metadata?.[2]).toEqual({ literalTrailingUnderscore: true })
+    expect(metadata?.[3]).toEqual({
+      literalLeadingUnderscore: true,
+      literalTrailingUnderscore: true,
+    })
+  })
 })
 
 describe('createRouteNodesByTo', () => {
@@ -663,6 +747,24 @@ describe('removeLayoutSegmentsAndUnderscoresWithEscape', () => {
       ),
     ).toBe('/foo/bar')
   })
+
+  it('preserves escaped trailing underscores after removing pathless ancestors', () => {
+    expect(
+      removeLayoutSegmentsAndUnderscoresWithEscape(
+        '/_layout/foo_/',
+        '/_layout/foo[_]/',
+      ),
+    ).toBe('/foo_/')
+  })
+
+  it('preserves mixed escaped leading and trailing underscores after removing pathless ancestors', () => {
+    expect(
+      removeLayoutSegmentsAndUnderscoresWithEscape(
+        '/_layout/_foo_/',
+        '/_layout/[_]foo[_]/',
+      ),
+    ).toBe('/_foo_/')
+  })
 })
 
 describe('routePathToVariable', () => {