Methods and structures using laser bonding for stacking semiconductor substrates are described. In one embodiment, a method of forming a semiconductor device includes forming a trench in a first substrate, and a bond pad on a second substrate comprising active circuitry. A top surface of the bond pad includes a first material. The first substrate is aligned over the second substrate to align the trench over the bond pad. An electromagnetic beam is directed into the trench to form a bond between the first material on the bond pad and a second material at a bottom surface of the first substrate.