A method is provided for bonding and interconnecting two semiconductor chips arranged on semiconductor substrates. HSQ (Hydrogen Silsesquioxane) or an equivalent material is used as a bonding layer and after bonding and thinning one of the wafers (or first thinning and then bonding), the bond layer is locally irradiated by an e-beam through the thinned substrate, thereby locally transforming the bonding material into silicon oxide. Then a via opening is etched through the thinned substrate and an etch process selectively removes the oxide from an area delimited by the bonding material or vice versa. The filling of the via opening establishes an electrical connection between the bonded wafers, that is equivalent to a connection obtained by hybrid bonding, but that does not suffer from the disadvantages thereof.