The present invention provides a method for removing or reducing the thickness of ultrathin interfacial oxides remaining at Si—Si interfaces after silicon wafer bonding. In particular, the invention provides a method for removing ultrathin interfacial oxides remaining after hydrophilic Si—Si wafer bonding to create bonded Si—Si interfaces having properties comparable to those achieved with hydrophobic bonding. Interfacial oxide layers of order of about 2 to about 3 nm are dissolved away by high temperature annealing, for example, an anneal at 1300°-1330° C. for 1-5 hours. The inventive method is used to best advantage when the Si surfaces at the bonded interface have different surface orientations, for example, when a Si surface having a (100) orientation is bonded to a Si surface having a (110) orientation. In a more general aspect of the invention, the similar annealing processes may be used to remove undesired material disposed at a bonded interface of two silicon-containing semiconductor materials. The two silicon-containing semiconductor materials may be the same or different in surface crystal orientation, microstructure (single-crystal, polycrystalline, or amorphous), and composition.