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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I see that your machines use an external controller. Are both machines experiencing this issue? Are you using Simplify3D with a desktop computer or a laptop? Have you tried to use leveling with another slicer program or with the external controller? What happens when you try to level it?