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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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All of mine were printed in PLA. I'm sorry to hear that you're having trouble with the flanges. If you have any more info about your printer and settings, or close-up pictures of the pieces, I might be able to help.