With the release of xEdit 4.0, the process of cleaning your ESMs has been simplified quite a bit. Elminster – the original creator of xEdit who returned to release 4.0 – mentioned the new cleaning process in a post here which I used as source.

8.1.1 Instructions

  • Open Mod Organizer 2 and click this icon.
  • Enter the following:
    • Title: SSEEdit – Quick Cleaning
    • Binary: point at Your Modding Folder\Tools\SSEEdit\SSEEditQuickAutoClean.exe
  •  Click Add, then close the window.


We are now going to clean four of the five official ESMs, Bethesda’s master files:

  • Update.esm
  • Dawnguard.esm
  • HearthFires.esm
  • Dragonborn.esm

8.2.1 Instructions – Update.esm

  • Run SSEEdit – Quick Cleaning through MO2.
  • The plugin selection window will come up next.
  • Select only Update.esm and click OK.

Now the cleaning process will begin automatically and it will take a few minutes. Simply let it sit and do its thing until you see Quick Clean mode finished in the log, then you can close xEdit.

8.2.2 Instructions – Remaining ESMs

Repeat this exact process for the other three ESM files (Dawnguard, HearthFires, Dragonborn). Double-click the SSEEdit shortcut, always select only one ESM at a time, wait until the log confirms Quick Clean mode finished and close xEdit.

Do not attempt to process Skyrim.esm this way.

8.2.3 Additional Manual Cleaning

There are instructions here to manually clean some dirty edits that won’t be caught by xEdit’s quick cleaning procedure. Only one of the edits can affect actual gameplay though, so we won’t bother with deleting the other two which are simply left-over test records.

  • Run SSEEdit.exe through MO2 (not the QuickAutoClean version).
  • In the plugin selection, check only Dawnguard.esm and hit OK.
  • Wait for xEdit to load up the plugin before you continue.
  • Once xEdit returns the message Background Loader: finished you may proceed.
  • Right-click anywhere in the left pane and select Apply Filter.
  • Change nothing in the window that comes up, but simply click Filter to confirm.
  • This will take a moment and you need to wait until it is done.
  • Double-click Dawnguard.esm (now displayed in orange) and double-click Cells.
  • Only one cell will be listed – 00016BCF RiftenRaggedFlagon. Select that cell.
  • Scroll down until you can see the conflict in the line marked red.
    • As you can see, Update.esm removed one Encounter Zone-related record here but it is re-added by Dawnguard.esm.
  • Right-click RiftenRatwayZone [ECZN:0009FBB9] in Dawnguard.esm and select Remove (see picture below).
  • There will be a warning, simply click Yes.
  • Close xEdit. When asked to save your changes, only Dawnguard.esm should appear in the list and it should be checked.
  • Click Ok. You’re done!


While the process of cleaning your master files is not particularly time-consuming once you’ve got the hang of it, we wouldn’t want to repeat it for no reason. Right now those cleaned ESMs are in our Data folder where they are going to be replaced with uncleaned ones everytime you verify the integrity of the game files through Steam or an update for SSE goes live. To prevent your cleaned ESMs from getting overwritten, we will simply install them through Mod Organizer 2.

8.3.1 Instructions

  • In MO2, create an empty mod (here).
  • Name your empty mod Official Master Files – Cleaned and hit OK.
  • Navigate to your Data folder and copy Update.esm, Dawnguard.esm, HearthFires.esm and Dragonborn.esm.
  • Right-click Official Master Files – Cleaned in your mod order and select Open in explorer.
  • Paste the four cleaned ESMs.
  • In MO2, move your new “mod” below the ESSENTIAL MODS separator (above SKSE – Data 2.x.x).

The ESMs in your Data folder (displayed at the top of your mod order in MO2) will be overwritten as you can tell from the silver lightning icons that now appear under Flags.