As Michael said, making areas transparent based on the colors of the pixels in those areas is called ‘keying’.
For basic information about keying, see “Keying overview and tips” in After Effects Help.
Unfortunately, unless you’ve shot your footage with keying in mind, it’s unlikely that you’ll be able to do good keying work. You may end up defining transparent areas in a much more tedious fashion: rotoscoping. In this context, rotoscoping is the drawing of masks around foreground objects and animating those masks—sometimes manually, frame by frame—to separate the foreground from the background. (Often, even footage that was shot well for keying requires a little fine rotoscoping work to clean up some pieces or some rough rotoscoping beforehand to draw garbage mattes. It’s hard to avoid rotoscoping.)
For basic information about rotoscoping, see “Rotoscoping introduction and resources” in After Effects Help.
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Todd Kopriva, Adobe Systems Incorporated
putting the ‘T’ back in ‘RTFM’ : After Effects Help on the Web
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