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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'm using slic3r with no problem at all, I've tested it on Cura with no problem as well. I've never used Simplify3D or ReplicatorG so I can't help with this. If they not intersect the base, slicer may tell that object is not manifold - this is why I did it. This is designed with Blender, I can send you editable files, just PM you email to me. Thanks.