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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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Sorry, I haven't used Slic3r much. Is Wipe selected? You can add " Retract amount before wipe" if blobs are the issue. You can always print the individual pieces in vase mode .85mm wide if you cant get the assembled file to work. I'm doing this with a .8 nozzle now and the parts look amazing!