System and method for bonding semiconductor substrates is presented. A preferred embodiment comprises forming a buffer layer over a surface of a semiconductor substrate while retaining TSVs that protrude from the buffer layer in order to prevent potential voids that might form. A protective layer is formed on another semiconductor substrate that will be bonded to the first semiconductor substrate. The two substrates are aligned and bonded together, with the buffer layer preventing any short circuit contacts to the surface of the original semiconductor substrate.