This paper deals with wafer temperature uniformity control essential in rapid thermal processing (RTP). One of the important control objectives of RTP is to keep the temperature over the wafer surface as uniformly as possible. For this, a discrete time state equation around the operating point is first identified by using the subspace fitting method, and a multivariable LQG(Linear Quadratic Gaussian) controller is designed based on the identified model. Simulation and experimental results show improvement in temperature uniformity over the conventional PID method.