Preheat the oven to 350 degrees F (175 degrees C).

Beat 3 yolks together in a bowl until smooth; set aside.

Whisk 3/4 cup sugar, cornstarch, and flour together in a saucepan until thoroughly combined; whisk in water, lemon zest, and lemon juice. Bring to a boil over medium heat; reduce heat to a simmer. Add egg yolks and butter; whisk until filling is smooth and thickened. Divide hot lemon filling among crusts.

Beat egg whites, remaining 1/4 cup sugar, and almond extract together in a glass or metal bowl with an electric mixer until meringue is fluffy and holds stiff peaks, 1 to 2 minutes. Top each pie with about 1-inch meringue; spread into decorative swirls and peaks with a spatula, completely covering filling with meringue.

Bake in the preheated oven until meringue is lightly golden brown with darker brown peaks and swirls, about 10 minutes. Cool before serving.