After the cookies have cooled completely, store them in an airtight container.
My mom will often bake cookies, and freeze the baked cookies. My parents eat them right out of the freezer.
Ideally, I prefer the cookies to be soft and freshly-baked. If I am not going to bake all of the cookies at once, I will form the cookie dough batter into balls and freeze them individually on a plate in the freezer. I then transfer the frozen dough balls to a Ziplock bag or Tupperware in the freezer, and pull out a few whenever I feel like baking some off.
If I am already using my oven for dinner, I will often throw a few cookies in there after my dinner is done cooking and set my timer for an additional 12 minutes. Then you have an amazing freshly-baked dessert ready to go.