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'll find that the files don't often import into Slic3r in the correct orientation. Always try to get the big flat side facing down. There are also a bunch of images included with the downloaded where he shows the proper orientation for printing some of the parts.