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.
Firstly thanks to all that suggested DesignSpark Mechanical. I've largely moved to it from sketchup and find many things so much easier now.
Also wanted to share a tool I found for repairing STL files. There's a file I downloaded from thingiverse that I just couldn't get to print and couldn't figure out why. As it was just one part in a 30+ part model and I'd already spent a week printing bits, I couldn't just give in. I found MeshFix (https://sourceforge.net/projects/meshfix/files/). It's a windows only command line tool. Just run "meshfix.exe -j brokenfile.stl" and it will attempt to repair your model.
Also found some online repair tools, but the only one that could fix the part was meshfix. Hopefully helps someone else out at some point.
Where I've had an issue recently though has been with STL files I've gotten from others that have errors and cause problems printing due to surface holes, internal faces, etc, etc. Opening up someone elses design and finding and fixing the issues can be painful