An electromagnetic wave irradiation apparatus and methods to bond unbonded areas in a bonded pair of substrates are disclosed. The unbonded areas between the substrates are eliminated by thermal activation in the unbonded areas induced by electromagnetic wave irradiation having a wavelength selected to effect a phonon or electron excitation. A first substrate of the bonded pair of substrates absorbs the electromagnetic radiation and a portion of a resulting thermal energy transfers to an interface of the bonded pair of substrates at the unbonded areas with sufficient flux to cause opposite sides the first and second substrates to interact and dehydrate to form a bond (e.g., Si-O-Si bond).