We present finite element simulations of fluid flow, heat transfer, and chemical reactions in axisymmetric rapid thermal processing (RTP) configurations. A new approach to simulating radiation heat transfer between lamps, substrates, and system walls is described. The method accounts for multiple reflections and readily allows the inclusion of temperature, radiation wavelength, and materials specific emissivity parameters. The influence of system geometry, lamp power profile, substrate and wall emissivity parameters, and process gas flow upon RTP performance characteristics is illustrated through examples. Transient flow and heat transfer simulations are used to identify operating conditions where flow recirculations are avoided. The further use of physically based models in the design and optimization of RTP systems is discussed.