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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It's designed for m3 screws. Try running a screw through the holes first to cut the thread, it will make your life easier. Alternatively if you have an m3 tap handy, use it to thread everything.