Just asking, I'm pretty curious.

A small search before asking?

http://www.uesp.net/wiki/Tes3Mod:Cleaning_Mods

Had found only this:

https://moddinginmorrowind.wordpress.com/2012/07/23/modding-tutorials-cleaning-mods/

http://www.nexusmods.com/morrowind/mods/3870/?tab=2&navtag=http%3A%2F%2Fwww.nexusmods.com%2Fmorrowind%2Fajax%2Fmodfiles%2F%3Fid%3D3870&pUp=1

:

damn, cleaning mods in tes 3 is pretty hard. I won't do it. I hate dos and everything it is. Especially when you click on the program and it just closes himself with no info, nothing at all. Wonder why no one made a tesedit equivalent...

Well, you have everything you need in the first link and it's not command line.

Every command line program does that. To use it correctly, shift + right click in data files folder where you have tes3cmd, select "Open command line here" and in the following window write "tes3cmd clean yourmodname.esp". I do not think that writing one text line is that hard...

Besides that, there are more ways to clean mods (although I would recommend to use them in addition to tes3cmd, not instead of it).

Of course you do not have to do it. But most people will write you in commends that your mod requires cleaning. Besides that, your mod might cause a lot of trouble if you will not clean it.

using tes3cmd is really not that hard, if you are able to do basic computer user actions like browse file/folders and copy files, e.g.
1. copy tes3cmd.exe inside your Data Files folder
2. right click Data Files folder from Windows File Explorer, http://www.eightforums.com/tutorials/9702-command-prompt-open-windows-8-a.html
3. type tes3cms.exe clean modname.esp
(you can hit tab to autocomplete what you are writing in DOS console to easily find your modname)

or you can install a http://download.fliggerty.com/download-58-141 including the "tes3cmd clean selected" menu option and use Mash as shell for tes3cmd.

testool is also good for automatic cleaning http://abitoftaste.altervista.org/morrowind/index.php?option=content&Itemid=10&task=viewpost&id=48&-How-to-properly-use-TESTool

sorry for double quote, but I am unable to edit previous post
[EDIT]remember, every .exe related to Morrowind may require to be "run as administrator" to work on after-Vista Windows systems.
If Melchor's executable of mash does not work, give a try to Yacoby's http://www.gamesas.com/topic/1523088-which-wrye-mash-should-i-get/#entry24083468

Or if you are like me and shun typing in a command line because you are bad at typing and prone to typos, you cat create a simple batch file as explained here: http://www.fliggerty.com/phpBB3/viewtopic.php?f=9&t=5734

There is actually a http://www.theassimilationlab.com/forums/topic/14241-wipz-tes3gecko/ project and one of its features is to clean mods similar to what mod cleaning is when using TESxEdit I think.

That's the easiest way to clean mods via an integrated tes3cmd gui in Wrye Mash.

I've never use the "run as administrator" method for any .exe file(s) related to Morrowind, Oblivion, Skyrim in Windows7 and thus far never got an issue for the last 4-5 years.

Cleaning mods in Melchor's WMSA require tes3cmd to be launched from the Utilities tab since it doesn't have an integrated tes3cmd gui via the popup menu in the Mods tab in Wrye Mash.

ah, my bad, I stand corrected, I confused Melchor's version with Sharlikran's http://www.gamesas.com/topic/1449775-wrye-mash-thread-6/?p=23726683 which being a fork of Yacoby's has the tes3cmd menu option included

[EDIT]link fixed

How have I never heard this... so much simpler. Thanks, WH-Reaper.