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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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Ah, I'm with you. I think you're after the edit -> separate shells command in Meshmixer. I put two batteries in a file because they were originally not symmetrical, and I haven't got out of the habit yet!