A system and methods are provided for low temperature, rapid baking to remove impurities from a semiconductor surface prior to in-situ deposition. The system is configured with an upper bank of heat elements perpendicular to the gas flow path, such that when the substrate is heated, the temperature across the substrate can be maintained relatively uniform via zoned heating. Advantageously, a short, low temperature process is suitable for advanced, high density circuits with shallow junctions. Furthermore, throughput is greatly improved by the low temperature bake.