Prusaslicer has some pretty good stl manipulation tools built-in these days. You can merge, split, add common shapes, subtract shapes, etc.

From the outside looking in, it seems like you should be able to do everything you want right in the slicer.

I’ve found this to be preferable for working with existing stl’s (not as useful for editing) if you dont have the actual step files or 3mf files available.