While it is technically possible to treat major rust, it is better left to the professionals. If you leave small rust spots too long, they will completely eat through the metal. The entire area needs to be treated to ensure all evidence of rust is removed. A special rust treatment is then applied. Metal mesh needs to be cut to fill the holes and body filler used to hold it in place. The area is then sanded and painted the appropriate color. As you can tell, it's a complex process with expensive tool requirements, so the best way to remove severe rust from a car is by means of professional services.