We consider the recursive identification and feedback control of the rapid thermal processing (RTP) system where the asymmetry of the convective heat transfer coefficient, caused by gas flow in the chamber, is taken into consideration. The success of RTP depends on the precise control of water temperature by adjusting the strength of the heating lamps to minimize dopant redistribution as well as wafer warpage. An efficient method of recursive identification and optimal feedback control is developed by separating the radiation field from the temperature field of the wafer and converting the beat conduction equation for the wafer temperature to a reduced-order model by means of the Karhunen-Loeve Galerkin procedure.