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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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The layers shift when one of your stepper motors loses steps. It's actually pretty easy to create a pathologically jerky path that will cause this to happen in printers that otherwise seem properly tuned, so it is not too surprising that you'll occasionally run across a model that fails this way. Try lowering your printer's X and Y "jerk" values.