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MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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What slicer do you use? There's an add-on for Cura called 'Mesh Tools' that includes the option to split model into parts. While I haven't tried it on this one it may work. Just turn off the option to automatically drop all models onto the baseplate in case it splits it into more bits than you thought it would!