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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Hmm, maybe something isn't quite working right in your Z axis and you are getting uneven layer height. This can happen if there is a lot of friction in the Z axis and you are getting some stick-slip action as you move up. If it is just noticeable on the inside leafs, htough, they may be moving around as you print. Maybe your acceleration or "jerk" setting are too high?