My solution is one of the following:
1) Rendering straight
- Render out as TGA sequences with STRAIGHT alpha, not premultiplied.
- In After Effects, choose "ignore alpha" on all the multipasses you want to comp together (for the same CG object anyway).
- Import ONE of the passes again, this time with alpha channel, and put it on top of the other layers, set to "stencil alpha" mode.
That way you comp your layers without alpha channels at all, hence you don't worry about the anti-aliased and semi-transparent areas, and then you add the alpha on top like a cookie cutter. -No ugly matte edges!
2) Un-premultiplying in After Effects (same as above, but with premultilpied 3D renders)
- Import all the passes with alpha channel set to premultiplied.
- For each layers you want to disable the alpha channel on, add a "levels" effect. Instead of RGB, set it to alpha. Move the slider so you "crunch" the alpha and re-store the un-premultiplied image data.
- Apply the "stencil alpha" layer on top like a cookie cutter, as in previous example
(end alpha geekiness

- Jonas