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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So using Makerware you aren't seeing this issue during the Toolpath preview? Here is a screenshot of what I"m seeing - 4 layers, no roof, all four corners detached. http://1drv.ms/1eMV4n1http://1drv.ms/1eMV4n1

I loaded the cover.stl into Netfabb basic, did a "automatic fix" to the model, but doesn't seem to help. I'm running it through a few other programs to see if there is an issue with it....