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.
Do you have an open source printer? If so, I think your nozzle offsets may not be very accurate. You should be able to adjust them in the firmware for your printer. Do you have a heated bed? The Micro Catapult is recommended to print better in ABS. I hope this helps!