If they are raised, no problem, simply use dimendional fabric paint and a cocktail stick. It takes a bit of practice to get a line of regularly sized rivets this way, but if you are not happy with your rivets, simply scrape them off with the same cocktail stick.
If your model is going to be subjected to a lot of handling and if you will be using masking tape during painting, I'd suggest you 'seal' the rivets with a light coat of Future.
You should find dimensional fabric paint in any craft store, and some shops such as WalMart. The brand I use is Plaid. They come in all colours which is very useful as it helps having bright color paint to see what you are doing!
Now, if your rivets are sunken, I have no easy remedy at all... Maybe light touches with a drill bit???