Just render your object(s) out as a targa sequence with an alpha channel, you'll find it in the render settings. remember to set the "frame/animation extension" to "name.#.ext" and the frame padding to 3 if you have more than a hundred frames of animation. Then go to render-batch render. your images will be placed in the directory you specify under file - project.
Hope this helps..
And if you need to bring in your camera to mach up the animation in AE (if the camera has animation of course). select your camera and bake your animation keys, and save the file as a .ma file. Then AE will read it fine.