So I recently found out that After Effects CS6 doesn’t have the ability to use a black and white image as an alpha image. It will accept formats that already have alpha channels in them such as the PSD Photoshop format or the EPS Illustrator format and allow you to use their alpha channels as a matte using the effects>channels>set matte but AE won’t actually let you treat a black background as an alpha matte without the use of a 3rd party plugin. That is, unless you know the trick.
Now take your images into After effects. Place the black and white alpha image in one track, the red circle just below it, and you’ll want a backdrop image also, so that there is something showing through once we are done applying the alpha effect. You can see how this is set up below.
Next, you will want to apply your favorite key to the alpha matte and a matte choker if necessary for clean up. We are trying to remove the black from the picture. In this case, using color key to remove the background worked fairly well.
Finally, hide the track containing the alpha matte. Then add effect>channels>set matte to the track with the red circle. Make sure that the “Take Matte From Layer” setting is set to the alpha matte. Then change the “Use For Matte” setting to Luminance. Voila, you have tricked After Effects CS6 into using a black and white image as an alpha matte.