So when I'm working with illustrator files, I usually get the designs I need to animate in one batch illustrator file with each of my scenes on individual artboards. I've saved these individually, however on import in After Effects, each artboard retains the layers from the other artboards in the master illustrator file. How do I avoid this? I really don't want to scavenge through every layer in AE to see what I'll be working with.
Your best answer will be in the AE help system and usage documentation, THere's an entire section devoted to Illustrator importing and layering.
AE works based on a file level. Using multiple artboards in the same file is not advised.