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.
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.