A method for desorbing the surface oxide on a silicon substrate is performed by implanting particles such at atomic or ionic hydrogen into the oxide layer on the silicon substrate. The oxide is then removed by breaking the bonds between the silicon and oxygen atoms within the oxide. The bonds may be broken by heating the substrate, for example. The temperature to which the substrate must be raised is substantially less than the temperature required to desorb an oxide layer that has not undergone an implantation step. In one particular example, the particles implanted into the oxide surface are hydrogen ions generated by electron cyclotron resonance.