After the cupcakes have cooled, cut a small cone from the middle of each cupcake using a paring knife. Save the cone of cake to put back after filling.
Pour the minty ganache filling into a piping bag or plastic storage bag.
Fill each cupcake by piping about a tablespoon or so of the filling into the hole.
Place the little piece of cake back over the filling and push down a little. The frosting will cover it if it looks messy.
Transfer the mint chocolate chip frosting to a piping bag or a plastic storage bag and pipe a swirl of icing over the top of each cupcake and top with a mini chocolate chip.