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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 print with Repetier host using my own custom slicer ABS profile for a 0.5mm nozzle. No scaling, printed in ABS. Are you getting a raised lip around the holes by any chance? that could account for it. Not sure what to tell you otherwise heh.