If someone creates 'Masks' within a composite shot, is it possible to 'Export' the clip and have the Masks recorded in the actual 'Alpha Channel'.
? ? ? ?
Yes, with caveats.
You're not "saving the mask" you're creating a matte. The difference is a mask is drawn directly on layer X. A matte takes data from layer Y to mask layer X. Once you render your mask, you'll be using it to control a Set Matte effect.
So, ideally your masks are on a plane layer?
Only certain Export formats support Alpha. PNG image sequences (no sound), Cineform, Pro-Res, Uncompressed AVI (don't use this) and EXR Sequences.
The Export Queue probably already contains a built-in preset for at least one of these formats.
If you build your own export preset, look for "Channels" and switch RGB to RGBA.
Bear in mind you don't actually the Alpha. You can also export onto a black background.
Either way, once you save the footage out, you apply it by loading the footage and muting it, then adding a Set Matte effect to the layer you want masked. Choose your mask video as "Source Layer," set alpha to REPLACE and use a Type of Alpha if you rendered transparent or Luminance if you rendered to a black background.
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