Heat the oven to 325 degrees. Line 12 muffin cups with paper liners. Combine the graham cracker crumbs, 3 tablespoons of the sugar and melted butter in a small bowl.
Stir with a fork until combined. Reserve 1/2 cup and press the remaining crumb mixture into the bottom of the muffin cups. Bake for 8 minutes or until lightly browned.
Meanwhile, beat the cream cheese, cottage cheese and remaining 1/2 cup sugar in a large bowl at low speed until combined. Beat in the eggs, one at a time, beating just until blended.
Pour the batter into the muffin cups. Top with the apple pie filling and sprinkle with the reserved crumb mixture. Bake for 20 minutes or until the cheesecakes are lightly puffed and set.
Cool in the pan on a wire rack to room temperature. Refrigerate for 2 hours or until chilled. Remove from the muffin tins. Drizzle with the caramel sauce, sprinkle with pecans, and serve.