I am looking to animate characters like these in After Effects but I'm struggling.
I have them as Vector files and have been saving their arms, legs, bodies and eyes as different Illustrator files and then importing them into After Effects but this is extremely tedious, especially when I have to re line up all of the body parts again.
There must be an easier way to select the leg/arm and move them?
There's no need to save the parts as separate Illustrator files. Rather, if you organize them as separate layers within the same Illustrator file, you can import the whole thing as a composition with the layers intact.
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An approach I've heard about is to save out the files as raster-based images, jpgs, pngs, or psds. Group them by body part, heads in one folder, arms in another, and so forth. Bring into AE by importing as footage rather than separate files or comps. The advantage is supposed to be that you can quickly replace body parts by using time remapping. So, for example if you wanted to animate a mouth talking, you import all the mouth shapes into a single footage file and swap mouths by just scrubbing the time remap value and setting a hold keyframe on the mouth shape you need. This cleans up your timeline and makes the need for multiple parts unnecessary.