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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Have you tried enabling " retraction " and "z Hop" it lifts the nozzel away when travelling. Also you could enable the travel not to pass over built areas in your preferences. but I was able to print using z hop only.