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.
Just printed the board with 0.15mm layer height, and M3 bolts worked perfectly. They need to bite a little in the raspberry pi, but they do fit perfectly afterward.
I used 4x M3x20mm flat-head machine screws, the result is a very nice flush top.