For the crust: In a food processor, combine the flour, sugar, salt and butter. Pulse the processor until the mixture resembles fine sand. Remove the lid and add the ice water to the mixture. Run the processor just until the mixture rolls itself into a little ball. If the mixture is a bit dry, add more ice water by the tablespoonful until it comes together. Gather the dough into a ball. With a bench scraper or knife, divide the mixture evenly in half. Shape each half into a disk. Wrap each disk in plastic wrap and chill at least 30 minutes.
Cook's note: At this point you can keep the wrapped dough in the refrigerator for a few days or freeze for later use.
For the filling: In a saucepan, combine the pitted cherries and 1 cup water over medium-low heat for 10 minutes. In a small bowl, combine the sugar and cornstarch. Using a whisk, swirl the ingredients together, making sure that there aren't any lumps in the cornstarch. Add the sugar-cornstarch mixture and lemon zest to the cherries. Cook the cherry mixture until it comes to a rolling boil. Cook 1 minute more, until thickened. Allow the cherry filling to cool slightly while you prepare the crust.
Preheat the oven to 425 degrees F. Spray a 24 cup mini muffin tin or 2 (12 cup) mini muffin tins with cooking spray.
Roll the dough disks out into 10-inch rounds on a well-floured work surface. With a 1 1/2-inch round cookie or biscuit cutter, edge lightly dipped in flour, cut 24 rounds from the first rolled out disk. With a 2-inch round cookie or biscuit cutter, edge lightly dipped in flour, cut 24 rounds from the second rolled out disk. You should have a total of 24 (1 1/2-inch) rounds and 24 (2-inch) rounds for matching top and bottom crusts.
Gently fit the 2-inch dough rounds into the bottom of the prepared mini muffin tin. Make sure to pat down the bottom and the excess coming up the sides. Spoon about 1 heaping tablespoon cooled pie filling into each crust-lined cup. Fit the top of each mini pie with a 1 1/2-inch dough round, pushing down gently and sealing the bottom crust and top crust by crimping the edges together with a fork. With a sharp paring knife, make 3 small incisions on the top crust, to allow the steam to escape.
Bake until the edges are golden brown and the filling is bubbly, about 12 minutes.
Allow to cool on a wire rack, and then remove from the muffin tin.