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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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Looks like the files are not 'manifold' or a bit broke.  I ran it through NetFabb free and cleaned it up and had no problem.  Im using Slic3r in Repetier, which once sliced, had no holes and elongated nubs. :)  Just a heads up for others that may have some strange behavior from their slicers.