unless the bolts are obviously octogonal or hexagonal, your best bet is to try Dimensional Fabric Paint and a cocktail stick..!
This kind Fabric Paint comes in numerous colours - which is good since you can chose a colour that will stand out on the plastic of your model - and is being manufactured by numerous companies such as Plaid.
I bought some in Walmart, but the stuff should also be available in craft stores (needlecraft, cross-stitching and the like).
It takes a bit of practice to get a line of regularly sized bolts/rivet heads... But if you're not happy with them, you simply scrape them off with another stick. When happy with the stuff you've done, seal it with a light coat of Future floor polish.