Line a 24-cup mini-muffin tin with 24 paper liners.
Place semisweet chocolate in a plastic bag, seal, and pound into small pieces.
Microwave half the chocolate at 50% power for 1 minute, stir, then microwave again until melted, about 1 minute. Stir until smooth.
Transfer melted chocolate to a zipper-lock bag, snip the corner, and pipe into each muffin cup to fully cover the bottom. Freeze for 15 minutes.
Microwave peanut butter for 1 minute, stir in confectioners' sugar, softened butter, and sea salt until smooth. Transfer to a zipper-lock bag, snip the corner, and pipe over the chocolate base.
Melt remaining chocolate using the same microwave method, stir until smooth. Transfer to a zipper-lock bag, snip the corner, and pipe over the peanut butter layer.
Freeze for 30 minutes. Remove peanut butter cups from the tin and serve. Store extras in an airtight container in the fridge for up to 2 weeks.