Uninstall the game, delete the files left behind, reinstall the game then dont use mods. Guide to removing all 3rd-party mods and other files from your Skyrim installation- by torminater, wikified by Farlo The best way of course is to use your zip file that you made of the Skyrim Directory as you followed the Skyrim Installation Guide, just delete the whole directory and unpack the zip.
I'm looking for a good, reliable way to remove all of my mods from Skyrim. My game has gotten a bit cluttered with content, so I figure I want to start fresh with a vanilla Skyrim and just work toward getting a decent amount of mods that don't end up driving me insane. The last time I did this, I uninstalled Skyrim completely, but I'm not a big fan of losing my saves again, and there were still a few location mods that found a way to stick around through the second installation.
How To Uninstall Workshop Mods
Of course, there's always the possibility that I did something wrong last time, but I was wondering if there were any good ways to wipe the game of all mods without corrupting or deleting saves, or somehow damaging the game in any other way.