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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Sorry to hear you're having issues. ... this all comes down to your machine and/or slicing apps accuracy. . As it sounds like your machine is not able to deal with the fine clearances try uniformly scaling it up about 5% as that will increase the internal clearances. I hope this helps.