Which is the best tool for cleaning Skyrim plugin files?

Like I mentioned in my previous thread, objects such a glacier, dwarven spheres and even a small plant have appeared seemingly randomly in several of my interior cells. But they only show up ingame, not in the CK.. despite loading and reloading the cells. Unfortunately, nobody seemed to know what caused the issue. I think, it might have to do with vanilla objects that I might have accidentally deleted. At least in the case of the dwarven sphere. Though I have not touched any glacier, so where that piece comes from, I do not no.

Anyways, now I need a cleaning tool, to see if I can eliminate the issues this way.