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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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how do you unclog the nozzle? maybe to hot?
check if there is enough cooling, and the feeder gear is clean.

Skeinforge is not very easy to configure, Print-O-Matic seems to be easy but in most cases you're better with manual control.
maybe you can use the makerbot software.