Abstract: Controllers and associated methods for controlling a thermal reactor or other thermal semiconductor processors which include a heating element powered by a power source, and having profile thermocouples and spike thermocouples. One preferred method comprises the following steps: modeling thermal dynamic characteristics of the thermal reactor, the modeling step including providing thermocouple instrumented wafers in the thermal reactor, perturbing the thermal reactor by controlling the heating element using a stimulation sequence, and developing models based on changes in temperature created by the perturbations. The models are developed off-line and can include one or more models, such as a model of power versus spike thermocouple readings, a model of spike thermocouple readings versus profile thermocouple readings, and a model of profile thermocouple readings versus thermocouple instrumented wafer readings.