Preheat the oven to 400 degrees F. Line a large rimmed baking pan with foil and spray lightly with cooking spray.
Cut the peppers in half lengthwise and remove the ribs and seeds. Arrange the peppers on the prepared baking pan cut-side up.
Mix the cream cheese, Cheddar, bacon, Fresno pepper and milk together in a bowl until very well mixed and soft.
Put the mixture into a resealable plastic bag (or a disposable pastry bag) and snip a corner to make an opening a little less than 1/2-inch across. Pipe a line of the cream cheese mixture into each of the peppers (the filling should not fill the whole pepper; it will spread as it cooks).
Bake until the peppers are tender and the filling is melted, about 15 minutes. Serve hot.