Systems and methods are disclosed for bonding of substrates using microwave energy. In some embodiments, semiconductor substrates can be bonded through a thin interlayer metal to a metal substrate by using microwave energy. High intensity microwave energy is applied to the substrate assembly positioned within a microwave cavity. A process of selective heating can occur in the thin interlayer metal, resulting in melting of the thin interlayer metal to facilitate bonding of the two substrates. Some of the advantages associated with such bonding process are disclosed.