A wafer temperature control system is developed for rapid thermal processing (RTP) semiconductor manufacturing equipment. The control algorithm is based on a physical model describing the heat transfer effects in advanced RTP equipment. A model identification procedure is proposed to estimate the uncertain parameters of the model from a set of experiments. Through singular value analysis, the impact of equipment design on feedback controller development is studied. An internal model control (IMC) design methodology is used to develop a low-order multivariable feedback control algorithm. The feedback controller is coordinated with additional modules including feedforward control and gain scheduling to achieve improved performance and flexibility. The algorithms are applied to three different multizone RTP systems. Temperature controlled ramps are demonstrated from 20 to 900-degrees-C at 45-degrees-C/s with less than +/-5-degrees-C during the ramp at high temperatures and less than +/-1-degrees-C average nonuniformity during steady state as measured by three radially distributed temperature sensors.