Pitted roof from rust under vinyl top repair

Hi, wanted to ask members how to go about tackling the pits in the roof from rust on a vinyl top car. Would very much like to put another vinyl top on which I already have from legendary in dark green.can I seal this and stop the rust from coming back? I thought metal filled filler. Can you skim it flat with lead fill like the seems are on the pillars? Any help would be great! Thanks Chuck