A system and method for reducing pilot runs of run-to-run control in a manufacturing facility calculates an unbiased estimation of an independent model intercept based on a state space model associated with the manufacturing facility. A determination is made as to whether to perform a pilot run in the manufacturing facility. Upon determining that the run is to be performed, an indication that the pilot run is to be performed is generated. Pilot run data is received in response to the pilot run being performed, and the state space model is updated based on the received data.