A system for and method of processing, i.e., annealing semiconductor materials. By controlling the time, frequency, variance of frequency, microwave power density, wafer boundary conditions, ambient conditions, and temperatures (including ramp rates), it is possible to repair localized damage lattices of the crystalline structure of a semiconductor material that may occur during the ion implantation of impurities into the material, electrically activate the implanted dopant, and substantially minimize further diffusion of the dopant into the silicon. The wafer boundary conditions may be controlled by utilizing susceptor plates (4) or a water chill plate (12). Ambient conditions may be controlled by gas injection (10) within the microwave chamber (3).