Normally the stud stays in as the pump will come off with the stud in place.
If you have to remove a stud use two nuts hold the top nut with a wrench and tighten the bottom nut against the top nut. When tight just use a wrench on the bottom nut and remove the stud. If the stud comes out they use a nut welded on and you remove it with a deep socket. The stud is for alignment purposes so leave it in place. Just feel with your fingers around the edge of the pump when ready tap it with a hammer and screwdriver and remove it.