Cook brownies according to directions. Allow to cool and cut into 3/4" pieces.
In a large bowl, combine the vanilla instant pudding and milk. Whisk to combine for at least 2 minutes. Mixture will be thick
Add the peanut butter and vanilla extract and stir to combine.
Fold in the whipped topping. Refrigerate until ready to assemble the trifle.
In a large trifle dish, place 1/3 of the brownies on the bottom. Top with 1/3 of the Reese's peanut butter cups (save a few for the top), and top with 1/3 of the vanilla whipped cream mixture. Continue layering until you have three layers.
Refrigerate until ready to serve.