This tool was created to allow you to easily use different meshes/textures per race on Skyrim's playable races. By default for non-beast races there is only one texture used by males and one by females (Argonians and Khajit have unique textures). This tool doesn't do anything by itself. There are already mods that create a framework for this:

Unique Everything
Unique Bodies per Race
Unique Bodies per Race SE
VTF- Vampire Texture Framework

In that case why this is needed? Because Skyrim stores each unique NPC face in a pre-generated nif file. While you can set up separate paths for distinct textures for the body, these pre-generated face files will always load the texture from the vanilla path. This results in a severe case of face/body mismatch on all unique characters excluding the player. Fixing this would require extracting each npc's head nif file and editing the path to point to the new texture... and you'd have to do it for every mod in your load order that has NPCs. A tedious and practically impossible task. This is where this tool comes in. It will do that for you automatically in several minutes.

Pros of this solution:
- almost fully automated process (all you have to do is pack the generated files and load them as a mod in mod manager)
- fully compatible with character appearance mods (makes sure to use the latest version of your NPC looks)
- modularity (you can select which races to patch)
- safe to use (does everything in an outside folder, at no point modifies shape or tintmasks of the head)
- works with large load orders (number of plugins limited only by xEdit itself)
- high compatibility (produces just nif files)
- tailored to end user's specific mod choices (makes sure to always use winning overrides in your load order when reading data)
- supports all Men (including elders), Mer and Beast races and their vampire counterparts
- will not change the looks of your installed standalone followers that use their own custom body and textures

That beeing said I advise you to use this tool (and the above mentioned frameworks as well) if you have at least intermediate knowledge of modding.

Before we continue some useful remarks:
* Please note that this tool is not used to fix your grey face, black face or brown face bugs (no, they are not the same). You should resolve these type of problems before using this tool. Otherwise they will carry on to your patched faces (well, the grey face will). A short guide is available in the articles section of this mod page that hopefuly will help you get rid of them.
* Do not, I repeat DO NOT use '...Skyrim\Data' folder or your mod manager data folder as an output destination.
* When installing these updated faces do so in a way that will allow you to easily uninstall them later (like when you want to generate a new patch). The best way to do it is according to the instructions below. But even if you don't want to use a mod manager then at least have your facegen data packed in a bsa file (make sure nothing is overwriting it).
* This tool is designed to be run on your whole load order. There is not much sense in running it on individual files as it will skip records that are beeing overwritten by plugins loaded afterwards.
* You should use this patcher when you are content with your load order and want to start playing. Otherwise you will have to use it everytime you add new mods with NPCs in it (it doesn't take too long to run though).
* If you are using unique textures for only some of the races there is no need to select all the races for patching. Save yourself some time.
* If you are familiar with DynDOLOD the process is pretty similar here on the users end.


IMPORTANT TROUBLESHOOTING NOTE

If in the process of patching faces xEdit throws out an error saying "Error reading NIF block 0 NiHeader: Error in "NiHeader\Export Info\Author": Prefixed terminated string does not end with terminator" that means the mod uses a really old format (Skyrim NPC Editor?) for head nifs that can't be read by xEdit. To fix it run them through NIF Optimizer (select just 'Head Parts Only' box). If it's just one file, opening and saving it in NifSkope will do the same.

Installation:
- place the script 'Skyrim - NPC Facegen Patcher.pas' in the 'Edit Scripts' folder of xEdit

How to use:
1. Launch TES5Edit/SSEdit. Load your current load order.
2. Select all plugins (Ctrl+A).
3. Right click. Choose 'Apply Script...' and run Skyrim - NPC Facegen Patcher.
4. Select which races you want to patch.
5. Select a folder to extract files to.
6. Wait for the patcher to finish.
7. Go into the folder mentioned in step 5. and compress the 'meshes' folder with 7zip (or a tool of your choice). Name the archive how you want.
8. Place the archive in the downloads folder of your mod manager.
9. Install this archive with mod manager as you would a mod. Let it override conflicts.
10. Play!

How to uninstall:
Uninstall the archive you created via the mod manager.

Credits:

sfts - for devising a clever way of identifying nif blocks based on xEdit's 'NIF - replace string' script and letting me use his code

Pieron - for the original NPC Appearance Patcher

ElminsterAU and the xEdit Team - who made it all possible in the first place