A thermal processing system and method including scanning a line beam of intense radiation in a direction transverse to the line direction for thermally processing a wafer with a localized effectively pulsed beam of radiant energy. The thickness of the wafer is two-dimensionally mapped and the map is used to control the degree of thermal processing, for example, the intensity of radiation in the line beam to increase the uniformity. The processing may include selective etching of a pre-existing layer or depositing more material by chemical vapor deposition.