Coming from Shake/Nuke background where I could isolate areas such as the hair/ body / pants and key each area individually, how do people do this in After Effects without having to duplicate & mask the footage each time for each layer?
Is there a keyer where you can select a mask just within the key properties and specify "ok this key is for the hair, lets use this mask" etc..?
You don't necessarily need to use mattes to do this if you shoot a chroma key. Oh, you may still want to isolate certain parts of the subject to set up different keying parameters, but they're typically animated garbage mattes that are a lot faster, and won't drive you into the insane asylum.
Used in conjunction with one another, they can help you pull a pretty darned good-looking key. It also helps A LOT to light for chroma key (just a google away) and to avoid shooting HDV when chroma keying. It's the worst kind of video you can use for the task.
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If there is a way to do what you're asking, I don't know about it, but I'd love to hear it.
I just got done doing a music video with about 180 greenscreen shots and used the methods Dave refers to in his response.
This isn't the first question I've seen, by the way, where someone new to the software is trying to get out of using multiple layers of the same footage in After Effects. Although this may seem like a crazy workflow, it actually works perfectly well.
If you have a trouble spot in the footage where your general key settings don't work well, use a mask to isolate the area, duplicate the footage on a second layer, and make adjustments.
Also, let me recommend Red Giant's KeyCorrect Pro. Its light wrap function alone is tremendous.