Coat an 9 inch square pan with cooking spray and line the pan with foil, leaving a 2 inch overhang on the sides. Coat the foil with cooking spray.
For the chocolate layer: Place the chocolate chips, butter and sweetened condensed milk in a microwave safe bowl.
Heat for 60 seconds, then stir and heat for an additional 30 seconds or until melted. Stir until smooth.
Use an offset spatula to firmly press the chocolate fudge into an even layer in the bottom of the pan.
Place the chocolate layer in the freezer to set up while you prepare the peanut butter layer.
For the peanut butter layer: Place the peanut butter, butter and vanilla in a large microwave safe bowl. Heat in 45 second increments until melted.
Stir until smooth, then gradually add the powdered sugar to the peanut butter mixture while stirring constantly.
Pour the peanut butter mixture over the chocolate layer. Quickly press the peanut butter cups into the top of the peanut butter layer.
Chill until firm, then use the foil to lift the fudge out of the pan and cut into 36 squares.