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 found a setting in Slic3r that was doubling the amount of filament extruded on the first layer. Turned that off, also turned down the extrusion multiplier to 0.6 and reprinted. Now things fit!