A method of manufacturing a semiconductor device includes forming a first recess in a first wafer. The first recess is at a first front-side surface of the first wafer and exposes a first interconnect structure in the first wafer. A second recess is formed in a second wafer. The second recess is at a second front-side surface of the second wafer. The first recess is filled with a first polymer. The second recess is filled with a second polymer. The first front-side surface of the first wafer is bonded with the second front-side surface of the second wafer such that the first polymer is bonded to the second polymer. The first polymer in the first recess and the second polymer in the second recess are removed. A metal is deposited in the first recess and the second recess.