Hmmm, I see what you're saying. I don't think I've explained myself correctly though.
What I need is for the separate blocks to be physically modified, so that when it's all be merged together, they form a single, flowing physical construction. Rather than several constructions overlapping one-an-other.
Eg
Currently I have, lets say, a box with a cylinder sticking out of the top. They're two separate objects and I merge them into one. But from a physical point of view, it's still a box, with two faces to each side and a cylinder overlapping into it slightly. What I need done is the top of this box, to have the two faces deleted, then new faces created between the vertices of the box, and the vertices of the cylinder.
First Picture's what I have
Second picture's what I want
(Done them manually, but I have several of these to do for each of the hundred or so models and they're much more complicated than this)
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