I am tyring to set up a system where I can apply the same chroma key to a large amount of clips (hundreds of short clips).

I need to create an alpha channel so that when I compress it to flv it retains the alpha channel.

Keying in final cut pro is tedious. I have the keylight plugin for After Effects, which is incredibly effective, but I can't figure out a quick way to apply it to all the clips. I'm not too familiar with after effects, but I don't believe there is a simple way to do this.

Ideally, there would be a command line tool I could use. Or someway to add a filter to squeeze or compressor. Does anyone have any suggestions?