A higher-level controller can correct measured metrology data with residual error values as reported by a lower-level controller. This results in a more accurate process disturbance estimate. A method of control obtains, based on measurement sample definition, a first process variable of a system under control, determines a residual error using the first process variable and a first set point, controls the system using the residual error, obtains, based on the same sample definition, a second process variable, and adjusts the second process variable using the residual error. The method may also include determining, using the adjusted second process variable, one or more first set points for controlling the system by the low-level controller that may vary in correspondence with the sample definition.