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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 opened the file the very first time and it seems to very clear what to do...
On Configurations Tab you have Selectors (Click on the Cell next to the "Select" Field to open the Dropdown) where you enter your Build Volume, the Type of Heatbed you want and if you want to have Single or Double Z-Axis. After that you find the extrusion Length for the profiles underneath the configurator and all other parts on the third Tab.