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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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Suggestion, I was trying to make a card box, it made but was a single STL with both top and bottom and since I'm a newb I have no skill to split them apart. (they are too big for my printer bed)
If you can add a step / setting for printer dimensions and automatically offer to make the two objects as two STL, that would work.