In this video, the Web Guru (https://webguru.info) will show you how to import layered Adobe Illustrator files directly into Adobe After Effects. For this to work properly, you must make sure your artwork is organized onto multiple layers inside of Illustrator before you import to After Effects. Watch the video for full details.
You can also read the full tutorial on the Web Guru blog: Importing Layered Illustrator Files into After Effects