Touching in the damage as you describe will never win any awards for prettiness, but it can do an excellent job of preserving the panels against further rust pitting. You’ll first need to remove the scabby paint and as much of the rust underneath as possible. For the smallest nicks, we’d suggest the tip of a pen-knife. For damage up to about a centimeter in diameter, a small grinding stone in a drill or Dremel works well. For larger areas, use a polycarbide abrasive wheel in a drill or grinder. Note that this will leave tiny scratches in the surrounding paint, so we don’t recommend it for small patches.
Remove rust and paint around the initial damage until you get to sound primer and bright metal. In many cases, you’ll find that rust has eaten deeply into the metal around the center of the damage. It’s not really practical to grind deeply into the panel to chase this out. Leave it for the next stage – a chemical rust remover. There are two basic types: an aggressive phosphoric acid-based confection such as Jenolite, or a safer non-acidic alternative such as Bilt-Hamber Deox-Gel. Apply according to the instructions supplied with the product you’re using.
For good measure, particularly if you’re not convinced that you’ve purged the rust from all nooks and crannies, follow the rust remover with a layer of rust converter such as Rustbuster fe-123 or Bilt-Hamber’s Hydrate 80. Always wipe off excess converter from surrounding paint while it’s wet – it sets rock solid when dry.
You can now apply primer and colour top coat. A top coat on its own is unlikely to prove weatherproof for long. Use a soft, sable-type artist’s brush for the smallest areas and a 1/4in or 1/2in natural bristle brush for larger areas. Brushing paint can be applied straight from the can, but test first to see if it needs thinning with cellulose or, in the case of polyurethane (synthetic) enamel, white spirit. If you have an aerosol, spray some into the cap of the can and let the thinners evaporate until it’s the right consistency for brushing.
When the paint has fully hardened (this may be up to a week for synthetic enamels in winter) you can rub it down carefully with a scrap of fine wet-and-dry paper and polish it so that it blends nicely into the surface of the existing paint. If the original paint coat is perilously thin, however, it’s probably best to leave it alone.
You can use masking tape to avoid scratching adjacent paint when de-rusting.