Replace the piece you removed and frost over it. Or, if you want more filling, eat the piece you removed and pipe directly over the hole, as shown below.
Fill Using a Piping Bag
Fill a piping bag with your filling, stick the tip into the center of the cupcake, and fill. This method only works with light, airy cupcakes like angel food cupcakes. If your cupcake is too dense, you’ll end up with a filling mess all over the place.
Remove Cores Using a Cupcake Corer
Use a cupcake corer instead of a knife to make holes in the cupcakes. It’s a fun little gadget that speeds things up a little bit if you are filling a lot of cupcakes at once or if you want to involve younger kitchen helpers in your baking.