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MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.

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Wouldn't call myself an expert at dual printing, but I would imagine separating the shells in meshmixer, or something similar, would get you the separate stl files. The trick would then be lining them up in your slicer..