Multimatte is a script for After Effects that makes a new layer with the combined alpha channels of several other layers.
Select one or more layers, run the script, and you'll get a new multimatte layer at the top of your timeline.
It uses the Set Matte effect, which works best with shape and text layers, and .ai layers with their 🔆 switch turned on. If any of your selected layers won't play nicely with Set Matte (maybe because they're a bitmap layer) Multimatte will give you the option of skipping them or fixing them before it does it's stuff.
The Multimatte User Guide, including installation instructions, is here.
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After Effects Script