Bottom sides of two semiconductor substrates are brought together with at least one bonding material layer therebetween and bonded to form a bonded substrate. A cavity with two openings and a contiguous path therebetween is provided within the at least one bonding layer. At least one through substrate via and other metal interconnect structures are formed within the bonded substrate. The cavity is employed as a cooling channel through which a cooling fluid flows to cool the bonded semiconductor substrate during the operation of the semiconductor devices in the bonded substrate. Alternatively, a conductive cooling fin with two end portions and a contiguous path therebetween is formed within the at least one bonding layer. The two end portions of the conductive cooling fin are connected to heat sinks to cool the bonded semiconductor substrate during the operation of the semiconductor devices in the bonded substrate.