MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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In S3D I had to reduce extrusion width on the gears. For my 0.4mm nozzle S3D defaults to 0.48mm extrusion width. Decreasing it to 0.4mm or even 0.35mm should solve that problem. I think I opted for 0.35mm as it allows for better infill in the teeth of the gears. The extrusion width can be reset to default after those parts are printed.