A method for reducing the roughness of a free surface of a semiconductor wafer that includes establishing a first atmosphere in an annealing chamber, replacing the first atmosphere with a second atmosphere that includes a gas selected to and in an amount to substantially eliminate or reduce pollutants on a wafer, and exposing the free surface of the wafer to the second atmosphere to substantially eliminate or reduce pollutants thereon. The second atmosphere is then replaced with a third atmosphere that includes pure, and rapid thermal annealing is performed on the wafer exposed to the third atmosphere in the annealing chamber to substantially reduce the roughness of the free surface of the wafer.