When I import the file into After Effects CS6 I only see a black scree and you can move the squares. What am I doing wrong?
If your illustrator art is just black lines it will be hard to see unless you change the background color.
A little more info about your AI files would help. You can import as footage or, if the AI files are layered importing as a comp may be a good option.
The top pic. is a Ai file.
Well here is what I do in Ai I have a white background create a few squares and a text, all in different colors. I am not using black. I same the file and then import it in After Effects and choose to keep layers. And I all I get is a black square with non of the graphics that I created.
In CS6, the import creates groups within the layer. You should be able to open those groups and do some manipulation.
If you're looking to split the objects into separate layers, then you need to go back to your Illustrator file and in the layers use the "Release to Layers" menu command. That will give you individual layers in AE. Tutorial on that method: http://illustrator.digitalmedianet.com/articles/viewarticle.jsp?id=309 23