Can I change the prefab for CharacterController?

Of course you can, what you need to do if you are using the one Unity gives you from the start.. go to the Hierarchy and select your CharacterController; it should of created Graphics object underneath that. Click on the a Graphics object and then in the Inspector you should see a section called something like Mesh Filter or whatever the shape is. This is where you need to be, just set your mesh from the capsule to something else. You literally just drag and drop the mesh into the place where the capsule is or you can click on the menu option next to it and browse for a new mesh.

If you need more help let me know.