you have to choose import layers when you import your file instead of merged layers. you hit import, then choose your file, then it will give you an option of whether or not you want to import the file as merged layers (all layers are 1 image) or individual layers. you can select the layers you want to use. if that doesn’t work, try looking at your file in Illustrator and make sure that the layers are not merged or grouped there.
hope that helps.