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 didn't have any trouble bridging the windows with my rep 2 and, yes, the windows print separately. Be prepared for some time. The first layer alone took me 6.5 hours in medium. I switched to the low setting for the rest but the second layer still took 4.5 hours. Looks great though!