MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I could be wrong, but your system with A parts and B parts don't seem to work. Just making 4 A units worked fine for me. (although our launch isn't until Aug 1, so I won't know for certain until then.) Your assembly part with rods, nuts, etc just uses 4 copies of the A unit.