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An alpha channel is what removes the background. ProAnimator renders with an Alpha channel by default but you may have turned it off. There are two things you need to do to make sure the alpha channel ends up in the final movie.
First, you need to make sure that the Alpha Channel checkbox is checked in the Output Panel.
Second, if you are rendering to a QuickTime movie, the compressor must be set to "Animation" and "Millions of Colors+". The "+" means it will render with the Alpha Channel.
Be sure that you Do Not use a compression type such as DVC, HDV, MPEG, JPEG or any other that does NOT support an alpha channel.
If you are rendering to an AVI file, use the Uncompressed option.
Once rendered, make sure that the program you are importing the file into (your Video Editing or Compositing program) is handling the Alpha Channel as Straight or Unmatted.
For example, if you are working with Sony Vegas, you will have to select your ProAnimator track, and right click to select "Properties". Under Properties, find "Alpha Channel" and you will be able to select the Alpha Channel as "Straight".