How to create a mask on individual frames of a video in Photoshop CS5 extended

I am working on a video piece and I need to mask out a moving figure throughout the entire video, what is the best way to to this?  I know that I can import the video frames to layers in CS3 and then create a mask on each frame, but there are thousands of frames - and when I render the video from the animation it is slow to run in quicktime.  Even if I were able to edit each frame, it seems like there should be a better way... I'm not terribly familiar with using Photoshop to edit video, maybe there is another program that would do what I want in a better way?
Any suggestions would be greatly appreciated.

This sounds like something Adobe Edge would be perfect for if it would just support video importing.
I created a mask over a video in Flash, but I had to convert the background video (which is masked) from mov to flv. Then you import it into Flash and stick the transparent PNG on a top layer for a mask. You can also animate the mask in Flash somewhat... more so if it's a vector object.
Result: Http://www2.avatarix.com/manatee
I would prefer to do this in HTML5 though... which is what Adobe Edge is for. But I can't figure out how to import video into Edge. I've tried 5 different video formats... webm, ogv, mp4, mov and flv.
Hoping this will be a feature when it's finally out in the market.
The struggle continues.

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