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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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Ok, I brought the cover.stl into Autodesk 3D Print Utility as it has an auto-fix feature for STL models. It had to perform 41 repairs on the part (what the repairs were, it won't tell me sadly). I re-saved the STL, re-imported back into Makerware, and it appears fixed now (screenshot: http://1drv.ms/1g4H0KQ)http://1drv.ms/1g4H0KQ).