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MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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I'm sorry to hear that you are having problems with slicing the motor_gear_fixed. I ran all of the STLs through the Netfabb cloud repair service before posting to make sure that there weren't any issues with them. Netfabb does not show any issues with that STL. Maybe try downloading it again to see if that helps. I stopped using Slic3r a while ago because it was too slow and had issues with complicated models (that may have changed in recent versions). I use kisslicer (free version works great) or craftware(free beta works great) or Simplify3d (expensive but works great). I tried slicing it with the current version of Slic3r that I have on my PC, version 1.1.4, and it sliced perfectly. There is a hole on the side that of that gear for a set screw. Is it possible that is what made it appear broken?

I hope this info helps. Good luck with printing and building this. It is challenging but fun. Post a "Made" when you get it done!