I'm really killing this description, but I think I just figured it the proper analogy:

Say the CAD designer creates a bolt and a nut. But they wind up "joining" the two separate objects into one object, when they export the .step file. So, in MOI, I can normally jut hover over either the nut, or the bolt, and the program will recognize that it is a separate object. I can then select it, type in a new name, and presto! it's now got its own layer.

So, the same issue applies here. But in this case, I have hundreds of small parts which would need the same treatment.

Does this make any greater sense, now? I'm sorry for leading you down the wrong path, as I wasn't trying to have MOI break apart the actual surfaces of the objects.