Abstract: A system for controlling a thermal reactor is disclosed that characterizes the thermal reactor with a reactor model that indicates behavior of the thermal reactor and of a load contained in the thermal reactor and that accounts for interaction among a set of heating zones of the thermal reactor. An online reactor model is then determined that estimates the thermal behavior of the load based upon an online input power to the thermal reactor and upon an online temperature indication from the thermal reactor. A time varying temperature and reactant flow recipe is determined that minimizes end of run parameters on the load. A multi-variable controller is employed to minimize temperature deviations of the load from a predetermined temperature recipe or time varying trajectory.