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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 just finished joining all the modules and exporting it as a single STL file. (I envy your build volume!!)
-BTW, I don't use STEP files. This is the one Thingy that I will only upload as STL.