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Well it's very hard to tell. Pretty much anything you can do in photoshop you can do in after effects with a bit of patience. But usually it depends a lot of the exact video you have.
Check out some tutorials online if you want a demonstration of what you can do with after effects, and what it takes to get there. videocopilot.net is a good place to start.
Yes, you can change eye color and remove blemishes from skin with After Effects.
There are many ways to do this sort of thing in After Effects. Here are a couple of suggestions:
To change eye color, use the Change Color effect. You can use masks on an adjustment layer to isolate the areas that the effect affects. You'll probably end up playing with blending modes to blend the result in with the original.
To remove blemishes, you can use the Clone Stamp tool to sample a patch of clear skin and use it over the blemish, or you might just end up changing the colors of the blemishes.
I recommend starting by going to the After Effects Community Help and Support page. Work your way through the material in the "Getting started" section. Then, after you've gone through those basic materials, come back here with detailed questions.
Digital makeup can be as easy as keying the skin tone and applying defocus or blur operations, and as hard as rotoscoping selected areas and tracking on a patch to cover blemishes/bags.
It all depends on the shot and it is not really something for beginners. You may be better off paying someone to do this. Contact me off list if you're interested.
Doing photo real effects work in AE is technically the most difficult feat and demands an understanding of compositing that goes beyond the use of AE and beyond that of a still image. Natural phenomena, motion related phenomena and lens distortion are all things that need to be strongly understood in order to do this successfully. Like others have said it is not for beginners, but I won't discourage you. Just be aware this is not a weekend project, and by the time you're done with it and if it's successful, there's a lot of places in Hollywood where they will pay you to do that for the stars.
One final note. It sounds like you have photoshop. If this is a short clip, perhaps you might want to try loading the video in PS (yes, you can do that) and do it there. Go under window and hit animate for a timeline where you can do some basic compositing. Try it out. Mess around. Then, after you know you're serious and your comprehension of image manipulation has exceeded PS, THEN take a look at AE.
since a few years i can tell myself i've started to become somehow cosy to Ae but i still would not do a job on perfect plastic surgery in Ae.
People who do Composits, Animation, SFX in general are talking in Frames or Seconds which can take up hours, days or even months creating the desired results.
Cutting/Editing a Movie is another opposite and should stay in its own world.
compositing a few noticable Action Scenes is one craft, but in my opoinion the real peak in Compositing SFX is to make the effects NOT NOTICABLE and only making the scenes looking good, not real.
Compared to film editing it is the same with the "invisible edit": The edit tells the story... and this can seriousely take years ;)
but, it's nothing to be afraid of. the coolest thing about all this is that everyone, no matter how long someone is into its business, you never stop learning. i think this is the point which makes it worth to go on and on and beyond.