A system for controlling a temperature of a wafer processing substrate includes memory that stores first data indicative of first temperature responses of at least one first thermal control element. The first data corresponds to the first temperature responses as observed when a first control parameter of the at least one first thermal control element is maintained at a first predetermined first value. A first controller receives a setpoint temperature for the wafer processing substrate and maintains the first control parameter of the at least one first thermal control element at a second value based on the received setpoint temperature. A second controller retrieves the first data from the memory, calculates second data indicative of temperature non-uniformities associated with the wafer processing substrate based on the first data and the second value, and controls a plurality of second thermal control elements based on the calculated second data.