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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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Congratulations! Link to video is probably wrong. Never mind, the picture is pretty descriptive.

I suppose You have the printer connected directly to computer and sending gcode through COM port emulated on USB, right?

I had problem with circles when printing Marvin. Back than I thought it is gearbox backslash or some other mechanical problem. Than I experienced the same problem on my other machines too. Find out the problem is caused by communication through COM port. When circle is made of too many short lines the buffer in printer electronics will run empty before new commands can be uploaded.

There are two possible solutions:
1, Export the model to STL with longer lines (circles divided to bigger angles). You will loose resolution hence circles will seem like polygons, but should keep regular shape. Try to reduce the print speed when doing small holes too.
2, Print from SD card as the communication between SD card and electronics is either quicker than through COM port or the electronics can handle the buffer better this way.