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.
Did you pay attention to the recommended settings?
It should be a long slow print...
If the cubes are fused in a way that required a chisel, you probably printed to fast, or over extruded.
Better luck next time!
P.S. you may try v1. It has a 0.2 mm clearance between the cubes.