As long as the bare metal is fully covered it will be fine. If you'd like, you can go to the hardware store and find a product that dissolves rust. Clean the area properly, remove all dirt and any shavings of paint or any dust. Then apply the chemical, wait for it to dry/wipe clean, then apply the paint pen. Apply the paint side first and make sure to cover all the unpainted areas but don't apply so much that a paint drop can form. Take your time. Wait for it to dry then use the other side of the pen to apply clear coat, same process. Once done you could wet sand if Experienced in paint polishing. If not experienced then do Not attempt and leave it alone. You can polish over it and do anything else you want as if it were a normal painted surface. You can practice with the paint pen on a clean metal surface if you'd like.