Which is the best and safest method for cleaning an .esp-file?

The things that need to be fixed are mostly accidental edits made to interior cells while exploring them in the CK for inspiration.

Is there an existing walkthrough of this? Which program should be used?

Thank you very much in advance!!

http://skyrim.nexusmods.com/mods/25859/?. http://www.youtube.com/watch?v=UOQO2S6HDBw is a link to a video tutorial.