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.
I think this is the document (attached) mastabug was saying, in case you're not a member and can't access it. Also, if you have Marlin firmware, there is a whole section on Bed Skew Compensation with instructions on how to enter the values obtained by printing https://www.thingiverse.com/thing:2563185, but of course getting the frame as square as possible first is probably better.
Hope this helps.