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There might be an action in the actions panel that can export the individual layers as an image sequence.
There might also be a script that you can find online (try the Adobe Exchange: adobe.com/cfusion/exchange) that could do that as well.
Normally though if you choose to create a new video layer from a file it will not bring the video in as separate layers but instead as a video clip that you can work with. Choose Layers>Video Layers>New Video Layer from File. You could probably then use the selection and eraser tools to remove the areas you needed. You can then export the video file or image sequence back out of PHotoshop. That would work in CS3 and CS4.
After Effects is intended for Motion Graphics and light Compositing. It would be used in place of Photoshop in this case.