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 that several of the files, including Cockpit and below_cockpit, print a lot easier if you rotate -4.69 degrees on the X axis. The parts are not natively flat on the bed, requiring either a fine-tuned adjustment of the part, or in S3D you can use CTRL-L and click on a flat surface on the bottom of the part, and S3D will rotate the part to be flat with the bed.