Make and bake vanilla cupcakes according to recipe directions. After the cupcakes have cooled, frost with vanilla bean frosting. Cover the cupcakes and set them aside.
To make the Captain America Cupcake Toppers, roll out the red fondant on a clean and smooth surface. If the fondant is hard to roll, massage with your hands for a minute.
Using the largest round stencil (that is labeled "red"), cut out 24 red circles. Repeat with the smaller round stencil (that is also labeled "red"). Peel back the extra red fondant, roll it into a ball, and store in a zip-top plastic bag so it won't dry out.
Next, roll out the white fondant. Cut out 24 circles and 24 stars. Store the remaining white fondant in a zip-top plastic bag.
Then roll out the blue fondant. Cut out 24 of the smallest-sized circles, labeled as "blue" on the stencils. Store the remaining blue fondant in a zip-top plastic bag.
To assemble the cupcake toppers, dampen the center of one of the largest red circles with water, and place a white circle on top. The water will help hold the pieces together. Damped the center of the white circle with water, and place a smaller red circle on top. Repeat with the blue circle and the star. Repeat this process to make each topper.
Let the fondant toppers completely dry, then place one on top of each frosted cupcake.