I use several different methods.
If it is a raised pin mark, I use an exacto to cut it down ,then sand smooth.
if it is sunken, my method will depend on how visible the repair will be.
If on a floorboard for example, I may simply flood the little indent with liquid putty (think surfacer primer) and once dry, sand level.
If the area will be a prominent surface, I may use liquid cement, and chopped up bits of sprue, preferably from the same kit, and make some sprue glus, fill the void, then once dry it will sand like the surrounding plastic. Another option is to dig it out a little, then use two part polyester putty (Bondo), but this requires more steps, including a good primer over the porous work area.
Basically, trial and error until you find what works for you.