There are a few ways to do fondant pearls,but I find that the best-looking way is to do a combination of hand-rolling and using a mold.
First, make a snake of fondant, and press it into the pearl mold. If it sticks you can rub some crisco into your hands so that when you roll the snake out it will be slightly greased up and ready to pop right out.
Press the mold together and remove the extra that squeezes out of the seam.
Remove the pearl strand from the mold.
This is the point where one method of using the strand would be to take a knife or another pointed tool and press the ridge between the pearls out. I don't like the way that looks, though, so I re-roll them by hand. The mold gives you the right amount to roll for each one to have a consistent size.
Roll each pearl and put them on a piece of foam to dry. Once they're dried you can shake them in some pearl dust in a closed container if you want them to have a shine.