Cool. After cupcakes have cooled completely use a sharp knife to cut a hole into each cupcake, do NOT go all the way through the bottom. Save the piece that comes out of the hole and trim it so that it is a small "lid". Set next to the cupcake it came from.
Fill pastry bag. Fit your pastry bag with your tip and fill the bag with a multi-opening tip with chocolate frosting and pipe it on the top of the cupcake in a circle. Create a single layer over the top of the cupcake and then go around the outer edge of the cupcake 2 or 3 more times to build up the sides of the nest.