How about trying something like I described in this thread a while ago
You could potentially create some fairly complex ‘cutter shapes’ out of primitives using booleans - and then use them with modifiers to cut out the parts you want.
If you models are single colour - you might actually be to save the modified STLs and then reload them back in.
Failing that I would probably use Fusion 360 - although it is pretty slow for this sort of thing.
Blender is better for editing meshes - but then you might end up with a lot of trouble getting rid of non manifold issues.