I'm taking a guess here that you're importing an Adobe Illustrator file as a Composition to find all of your separate objects in your AI file are only on one layer inside After Effects. If that's the case, it's important to remember that AE sees no deeper than AI Layers. So, objects and sub-layers are all merged to AE.
If you only need certain objects to be seen as their own Layer in After Effects, you can promote them to their own respective Layers by creating Layers as needed and then moving object(s) as needed to new layers.
If you need all of your objects to be seen as their own layer in After Effects, you want to use "Release to Layers - Sequence" in the Layer pop-up menu to promote each object to its own sub-layer. Then you want to move each sub-layer to the root level of the document (so that they are no longer inside a Layer). It's probably worth taking the time to give your layers descriptive names while still in Illustrator. If your Illustrator file is complex, this will take some time to do.
If this is the first time that you've ever used Release to Layers, I recommend doing this in a duplicate Illustrator file so that you always have your original to get back to. If the original is named "filename.ai", then name the duplicate "filename_for_ae.ai" (or anything like that that easily identifies that it's the document for After Effects.
Again, I'm just guessing.
-Warr