Sandblast it......I'm of the minority judging from the posts above, but rust will always be there if you dont remove it. I wouldn't risk it coming back after you spend $1,000's on paint and bodywork. Epoxy primer or etch primer will adhere better to clean metal. That's for the exterior of the car, the underside is much more forgiving
If you're working on your plumbing truck or firewood hauler, prime right over it.