Line an 8x8 pan (or 9x9 works too) with foil and spray with nonstick cooking spray. Place 16 whole peanut butter cups in a single layer, lining the bottom of the prepared dish. Set aside.
In a medium or large microwave-safe bowl, mix together the chocolate chips and sweetened condensed milk. Microwave on half power, stirring every 30 seconds until smooth and melted, about 2 minutes. Pour the thick chocolate mixture over the Reese's and smooth the top.
Chop up the remaining 8 peanut butter cups and press the pieces into the top of the fudge. Let cool to room temperature, at least an hour, then refrigerate until set.
Remove the fudge from the pan by lifting the foil out, cut into squares, and serve.
Serving size will depend on how you cut the fudge. I like to cut it into 6x8, or 6x6 for larger pieces.