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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The answer depends on the slicer that you are using. The top should print fine with the outside surface flat on the bed. Some slicers will let you click the part of the print you want to touch the bed, while in others you have to rotate manually until the part lies flat.