The best thing is to export the FLA file from flash via File>Export Movie. And then make the appropriate compression selections (uncompressed files get very large). If you don't have the FLA file then you will need to import the SWF into flash or After Effects and from flash repeat what I stated in the first sentence after the swf is on the stage. From After Effects you would Import the SWF file, place it in a composition, and add the composition to the render queue. In the Output module settings do not leave it as "based on lossless" as this is the uncompressed version. click on this phrase and choose format options and then the appropriate compression settings. Video for Windows is the After Effects name for AVI.
Thanks for the reply. Basically, I'm exporting the FLA file to a Quicktime Movie and then using MPEG Streamclip to convert it to an AVI file. The media company we're using prefers an uncompressed AVI file, which ends up being 175MBs. This is for a huge LED stadium sign for a local state basketball team. The problem is that MPEG Streamclip has way too many options. Is there an easier conversion program or specific settings we should be using?