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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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Still not quite sure what the issue is... however I checked all the .stl's and there are no issues according to my mesh checker. These have been printed by thousands of people and the vast majority get a great result...

Having said that, if anyone has an issue with this type of thing, they all too often use Slic3r. It is a slicing app problem as it doesn't seem to deal with the complexity of some designs as well as other apps. Cura seems better and I never have issues with my MakerBot Print.