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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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are you printing off of the sd card or via the usb cable? sd card is the more reliable option.
aside from that you should really switch to another slicer, ReplicatorG is great to start off with (since it comes with the printer) but it's really limited in features and just clunky.