Cool muffins completely. Place a paper towel layer at the bottom of a container. Then add the muffins in a single layer and cover with another sheet of paper towel. The paper towels will help absorb any extra moisture that forms.
In the refrigerator
Transfer to a container (no paper towels needed) and keep in the refrigerator for up to 5 days.
In the freezer
Place muffins in a single layer on a cookie sheet or plate.
Place the tray in the freezer for at least an hour, until the muffins are frozen solid. Remove and place in freezer bag or airtight container. Be sure to label with the date (I like to add the best by rather than when it was made).
Notes
It is best to thaw in the refrigerator overnight.
You can enjoy cold, at room temperature, or warm slightly in the microwave (no more than 30 seconds)