Need help with using cleanitol

[Althiea]

Hey there,

I just recently installed cleanitol and I am trying to work out how to use it. Am I suppose to use it before installing the mods? I tried that by having the mods extracted into the plugins folder and then using the cleanitlist button, however it put all mods and files in the back up file and cleaned out my plugins, I used the undo to restore the mods, but I have no idea on what I'm really doing  What am I doing wrong?