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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Use 3D Builder (comes built into Windows 10) it does automatic model repair, and you can export to STL if your printer is not already supported for direct Ctrl-P printing. As to why this manifold issue happens: it's a common problem with models produced by composition in OpenSCAD and similar tools. I haven't found a sure way to avoid it all cases.