A method for preparing an oxidized surface of a first wafer for bonding with a second wafer. The method includes treating the oxidized surface with a solution of NH4OH/H2O2 at treatment parameters sufficient to etch about 10 Å to about 120 Å from the wafer surface, followed by treating the etched surface with hydrochloric acid species at a temperature below about 50° C. for a duration of less than about 10 minutes to remove isolated particles from the oxidized surface. This method cleans the wafer surface without increasing roughness or creating rough patches thereon, and thus provides a cleaned surface capable of providing an increased bonding energy between the first and second wafers when those surfaces are bonded together. This cleaning process is advantageously used in a thin layer removal process to fabricate a semiconductor on insulator structure.