diff --git a/src/app.js b/src/app.js
index 244a368d..f91634bc 100644
--- a/src/app.js
+++ b/src/app.js
@@ -31,7 +31,7 @@ import { getPkgIndexes, rawInstallPkg, fetchPkgReadme } from './package_mgr.js'
 import { ConnectionUID } from './connection_uid.js'
 import translations from '../build/translations.json'
 import { parseStackTrace, validatePython, disassembleMPY, minifyPython, prettifyPython, compilePython, reprStr } from './python_utils.js'
-import { SYSTEM_DIRS } from './emulator.js'
+import { SYSTEM_DIRS, visibleTree } from './emulator.js'
 import { createPyDevicesVM, enableSimulatorAudio, armSimulatorAudio, disarmSimulatorAudio } from './pydevices/runtime.js'
 import { showDeviceStage, hideDeviceStage, initDeviceStage, onDisplayResize, getDisplayConfig } from './pydevices/stage.js'
 import { resolveGalleryExample, rawStageGalleryExample } from './pydevices/gallery.js'
@@ -1236,7 +1236,9 @@ async function _raw_updateFileTree(raw) {
         console.log(err)
     }
 
-    const fs_tree = await raw.walkFs()
+    /* The simulator's runtime keeps folders of its own; a real board's are all the user's */
+    const walked = await raw.walkFs()
+    const fs_tree = (connType === 'sim') ? visibleTree(walked) : walked
     const delta = fsCache.reconcileListing(fs_tree, isSpecialPath)
 
     _updateFileTree(fs_tree, fs_stats);
diff --git a/src/emulator.js b/src/emulator.js
index 05451746..adc99cbc 100644
--- a/src/emulator.js
+++ b/src/emulator.js
@@ -6,12 +6,12 @@
  * This includes no assurances about being fit for any specific purpose.
  */
 
-import { MicroPythonWASM, SYSTEM_DIRS } from './transports/vm.js'
+import { MicroPythonWASM, SYSTEM_DIRS, visibleTree } from './transports/vm.js'
 import { loadVFS } from './python_utils.js'
 import { loadMicroPython } from '@micropython/micropython-webassembly-pyscript/micropython.mjs'
 import i18next from 'i18next'
 
-export { MicroPythonWASM, SYSTEM_DIRS }
+export { MicroPythonWASM, SYSTEM_DIRS, visibleTree }
 
 const T = i18next.t.bind(i18next)
 
diff --git a/src/pydevices/runtime.js b/src/pydevices/runtime.js
index be2295c4..f23a4d63 100644
--- a/src/pydevices/runtime.js
+++ b/src/pydevices/runtime.js
@@ -74,7 +74,7 @@ import os, sys
 # Absolute /lib, matching a board: the package manager finds the install
 # target by looking for a sys.path entry that ends with "/lib", and a
 # relative "lib" left it refusing to install anything on the simulator.
-sys.path[:] = [".", ".frozen", "/lib", "/utils"]
+sys.path[:] = [".", ".frozen", "/lib", "/utils", "/.shim"]
 from boarddev import env_set
 env_set("PYDEVICES_WIDTH", ${Number(width)})
 env_set("PYDEVICES_HEIGHT", ${Number(height)})
@@ -181,6 +181,8 @@ export function createPyDevicesVM(opts = {}) {
     const port = new MicroPythonWASM(loadPyDevicesMicroPython, {
         wasmURL: runtimeURL('micropython.wasm'),
         infoType: 'PyDevices Simulator',
+        // machine.py's home: on sys.path (see bootScript) but not in the user's lib/
+        shimDir: '/.shim',
         // The build is compiled with ASYNCIFY, so the VM can yield to the
         // browser instead of locking the tab up for the length of a sleep.
         asyncify: true,
diff --git a/src/transports/vm.js b/src/transports/vm.js
index 886f59cc..e65aba8f 100644
--- a/src/transports/vm.js
+++ b/src/transports/vm.js
@@ -12,6 +12,16 @@ import { Transport } from './base.js'
 const PYEXEC_FORCED_EXIT = 0x100
 export const SYSTEM_DIRS = new Set(['/sys', '/dev', '/proc'])
 
+/* Top-level entries the runtime itself needs (the interpreter's /tmp and
+   /dev, the emulated home, the shim folder below) but that are not the user's
+   files. They stay on the device; the File Manager just does not list them. */
+export const HIDDEN_ROOTS = new Set(['/dev', '/home', '/proc', '/sys', '/tmp', '/.shim'])
+
+/** Drops the hidden top-level entries from a walkFs() tree. */
+export function visibleTree(tree) {
+    return tree.filter((n) => !HIDDEN_ROOTS.has(n.path))
+}
+
 const MACHINE_MODULE = `\
 def reset():
     raise SystemExit
@@ -99,6 +109,7 @@ export class MicroPythonWASM extends Transport {
         this._inRawMode = false
         this._suppressedOutput = false
         this._fsPopulated = false
+        this._shimDir = opts.shimDir || '/lib'
         this._decoder = new TextDecoder('utf-8')
         this._writeQueue = Promise.resolve()
         this.info = { type: opts.infoType || 'MicroPython WASM' }
@@ -135,9 +146,13 @@ export class MicroPythonWASM extends Transport {
             try { this.mp.FS.mkdir('/lib') } catch { /* exists */ }
         }
 
-        // Always ensure machine module is present
+        // Always ensure machine module is present. It lives in shimDir, which a
+        // runtime can point away from /lib so the user's lib/ starts empty.
         try { this.mp.FS.mkdir('/lib') } catch { /* exists */ }
-        this.mp.FS.writeFile('/lib/machine.py', MACHINE_MODULE)
+        if (this._shimDir !== '/lib') {
+            try { this.mp.FS.mkdir(this._shimDir) } catch { /* exists */ }
+        }
+        this.mp.FS.writeFile(this._shimDir + '/machine.py', MACHINE_MODULE)
 
         // Interpreter state - sys.path, environment, imports - does not survive
         // into the fresh VM a reset builds, so this runs for every one of them,
diff --git a/test/browser/boot-file-tree.spec.js b/test/browser/boot-file-tree.spec.js
new file mode 100644
index 00000000..8cfcfc0c
--- /dev/null
+++ b/test/browser/boot-file-tree.spec.js
@@ -0,0 +1,33 @@
+// SPDX-License-Identifier: MIT
+//
+// The simulator's File Manager used to list the runtime's own folders (dev,
+// home, proc, tmp) and a machine.py in lib/ next to the examples. A fresh
+// simulator shows the examples, main.py and an empty lib/ for installed
+// packages, nothing else.
+import { test, expect } from '@playwright/test'
+import { connectSimulator } from './helpers.js'
+
+test('a fresh simulator lists only the examples, main.py and an empty lib/', async ({ page }) => {
+    await connectSimulator(page)
+    const rows = page.locator('#menu-file-tree .tree-row[data-path]')
+    await expect(rows.filter({ hasText: 'main.py' })).toHaveCount(1)
+    const paths = await rows.evaluateAll((els) => els.map((e) => e.getAttribute('data-path')))
+    expect(paths.sort()).toEqual([
+        '/',
+        '/00_touch_paint.py',
+        '/01_lvgl_counter.py',
+        '/02_lvgl_thermostat.py',
+        '/03_pdwidgets_dashboard.py',
+        '/04_pygraphics_shapes.py',
+        '/05_displaydev_raw.py',
+        '/lib',
+        '/main.py',
+    ])
+})
+
+test('the interpreter still has what it needs after the tree is trimmed', async ({ page }) => {
+    await connectSimulator(page)
+    await page.locator('#xterm').click()
+    await page.keyboard.type("import os, machine; print('TMP', os.stat('/tmp') is not None, hasattr(machine, 'reset'))\n")
+    await expect(page.locator('#xterm')).toContainText('TMP True True')
+})