For the Filling: Preheat Oven at 350°F. Using an electric mixer blend cream cheese on low speed in a mixing bowl. Use spatula to scrape sides and paddle of mixer. Add in the sugar slowly, and continue to beat until creamy. Add in vanilla extract and mix until blended. Add in eggs one at a time and continue to mix a lowest speed until eggs are incorporated in the batter.
Line muffin tins with paper liners. Place 1 vanilla wafer in bottom of paper liner. Pour the batter in each liner. Bake for 15 to 20 minutes or until top is slightly brown. While muffins are baking, prepare topping.
For the Topping: Mix sour cream, sugar and vanilla extract. After cheesecake muffins have finshed baking, let cool for about 15-20 minutes and then spread topping on cheesecake muffins. Replace in oven for 5 minutes. Remove from oven and let cool. Place in the refrigerator and allow to set. Serve and enjoy your Cheesecake Cupcakes.