If their minor you could probably use spot putty. Deeper pits I'd use a fiberglass based filler like Duraglass, I thing there's one also called RustOut. These are fiberglass resin in them but no hair.
Have you checked out zerorust.com website, alot of guys on here have been using it on there trucks, I haven't tried it yet myself. If it's just surface rust it really shouldn't be that rough once you remove it. Like I said above a filler type primer may fill small irregularities.
