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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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Thank you for the info!
I have tried to upload a repaired an a new version, but the black glitches are still there.
This are the parts which are left from the model i remixed.

Can you try out if one of the files prints correctly with your printer?

I sliced and printed exactly the file I uploaded first and it worked out without problems. (Slic3r + Repetier Host + selfmade printer)