before i start, i need to say that this program is in beta. "experimental" even. i personally have never had a problem with it, but that is not to say it could not happen. using this program, i have been able to play past many bugs which previously haunted me, and allowed me to complete missions i could not previously complete.
also, you might want to have a look at this TESV Edit video.
It is way too long and drawn out. To simplify,
1) Download TESV Edit. http://skyrim.nexusmods.com/mods/25859/?
2) Unzip the file anywhere, open the folder, then open TESV Edit.
3) Right click and choose "Select None" at the list which pops up, then check the mod, or master file that needs cleaning. (Dragonborn.esm, Dawnguard.esm, Hearthfires.esm, and Update.esm all need to be cleaned. Skyrim.esm DOES NOT NEED CLEANING, DON'T DO IT.) To simplify this, only do one mod or master file at one time.
4) Wait for the mod or master file to finish loading, then right click that file, and select "Apply filter for cleaning." (At the top of the program, it says "yes, this takes a while, just wait!) so wait. lol
5) after the filter has been applied for cleaning, right click the file again, then select "remove identical to master records." This will probably go very quickly.
6) right click the file yet again, but this time select "undelete and disable references.
7) close TESV edit. if everything went right, you will see one of two things. First, you might see the selection window load up again with only your file checked. this means you successfully cleaned a dirty file. Second, TESV edit might just close. This means your file did not nead cleaning.
8) in closing, the author of the video does not recommend blanket cleaning all your mods. i have a different attitude. if a mod shows up dirty, i clean it. if that means the mod doesn't work anymore (that hasn't happened yet, but i have seen at least one mod which specified it could not be cleaned in TESV edit.) then i ditch that mod. be really careful about which mods you install. for instance, the latest CBBE version already has remodeled female feet, and does not need a mod called "femfeet." Using these two mods together results in broken texture seams at the hips, and or feet. Another mod "NPC Hair Overhaul" is known to create the grey face bug, yet it still exists in its unfinished/unfixed form at Skyrim Nexus. don't try to make known troublemaker mods work for you.
Also, the previous question mentioned BOSS. BOSS automatically sorts your files, and gives a report, which includes some of the files need cleaning in TESV edit. If the mod is in the unrecognized area, it may still need cleaning, even though BOSS did not report it.