I would defer to more knowledgable people here, but in my experience you wouldn't want to completely remove the rust to create a totally smooth surface. I would scrape it with a small brush to remove excess rust, but if you leave it as a rough surface, the paint will bond better. I.e., paint likes a toothed surface, not a baby's-butt smooth one, so scrap the rust flat but don't anihilate it. Someone who knows what they're talking about is welcome to override my advice, though.

__________________
1987 300D, arctic white/palomino--314,000 miles
1978 240D 4-speed, Euro Delivery, light ivory/bamboo--370,000 miles
2005 Jeep Liberty CRD Limited, light khaki/slate--140,000 miles
2018 Chevy Cruze diesel, 6-speed manual, satin steel metallic/kalahari--19,000 miles
1982 Peugeot 505 diesel, 4-speed manual, blue/blue, 130,000 miles
1995 S320, black/parchment--34,000 miles (Dad's car)