Preheat oven to 350◦. Place 12 cupcake liners in a standard muffin tin. Set a vanilla wafer in the bottom of each liner.
Using an electric mixer, beat cream cheese until smooth, then add sugar and beat until light and fluffy. Add eggs, one at a time, beating after each addition. Stir in vanilla. Spoon cream cheese mixture on top of wafers, dividing evenly.
Bake until tops of tarts are puffed (there will be some cracks) and just starting to turn golden around the edges, about 30 minutes.
Let cool (tops of tarts will cave in), then carefully remove tarts from muffin tin. Refrigerate overnight.
Top each tart with a large spoonful of pie filling (you'll have some left over) before serving.