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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Correct, you need to add regular supports for the flanges. What's your nozzle diameter? The custom supports are .4 mm thick, so you should make sure that your Extrusion Width is set to .4 mm.