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.

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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.