A combination of a dry oxidizing, wet etching, and wet cleaning processes are used to remove particle defects from a wafer after ion implantation, as part of a wafer bonding process to fabricate a SOI wafer. The particle defects on the topside and the backside of the wafer are oxidized, in a dry strip chamber, with an energized gas. In a wet clean chamber, the backside of the wafer is treated with an etchant solution to remove completely or partially a thermal silicon oxide layer, followed by exposure of the topside and the backside to a cleaning solution. The cleaning solution contains ammonium hydroxide, hydrogen peroxide, DI water, and optionally a chelating agent, and a surfactant. The wet clean chamber is integrated with the dry strip chamber and contained in a single wafer processing system.