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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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You can definitely do that. You can use Meshmixer to cut the parts and then glue them together after they are printed. Here is a link to a tutorial on how to do this: https://www.youtube.com/watch?v=1Wzut-W2zTk.

Meshmixer can be found here: http://www.meshmixer.com/download.html