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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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I just looked at the preview in simplify3d, and it seems to be ok. I have enabled support material generation.

Maybe run it through netfab free or make printable, and/or try another slicer?