Im trying to get some footage that is on a green screen into a SWF with a transparent background.

I have aftereffects and flash cs4, what is the best way?

Have you tried rendering as an image sequence, in a format (TIFF, TARGA, etc) that supports transparency?

Not sure if Flash can import these formats, as I don't use Flash, but it's worth a try.

I did this once for a flash based website. I seem to remember I rendered the keyed footage to a quicktime animation with the alpha channel and then put that in the flash encoder which has an option to use the alpha channel. Something like that. I outputted a FLV that I imported into Flash.

Here is a tutorial which I reckon will help a little :)

gotoandlearn.com - Green Screen Video Fundamentals (http://www.gotoandlearn.com/play?id=93)