How do you touch up paint on a car with rust?

Be sure it is rust first--rust is usually brown or dark red in color, often flaking and may include tiny holes. The rust must be removed before applying paint otherwise the paint won’t adhere properly and the rust may simply return even if you do manage to paint the surface. You'll find more detailed help here: How to Remove Rust from a Car. Sandpaper off the rust before painting, then use rust-proof primer before adding the appropriate color of auto paint. Severe rust (big holes, pieces of car falling away, etc.) should be attended to by an auto body specialist; painting over it won’t solve the rusting problem.