The top crusts are where you can have a little fun, or you can keep things really simple. Any method from creating a top crust on a full sized pie you can just make smaller for topping your cup-pies.
For a simple top: Cut out 3" rounds from your pie dough. Create vent holes by cutting several slits in the middle of the dough. Place your dough on top of the filled tins. Use a fork to crimp the edges together with the bottom crust.
For a lattice crust: On a lightly floured surface, cut several long strips of dough out roughly the same size. Create a lattice pattern by weaving every other piece over every other piece. Once your pattern is complete, use a 3" cookie cutter to cut out the tops. Moving them over to the tin can be a little tricky, but I found using a metal pastry scraper to be the best way to scoop each top up and gently place it on top of each pie (as long as your surface was floured you should be able to do this fairly easily!). Once placed, gently crimp together the edges with the bottom crust.