A method of controlling processing of a substrate includes generating, based on a signal from an in-situ monitoring system, first and second sequences of characterizing values indicative of a physical property of a reference zone and a control zone, respectively, on a substrate. A reference zone rate and a control zone rate are determined from the first and sequence of characterizing values, respectively. An error value is determined by comparing characterizing values for the reference zone and control zone. An output parameter value for the control zone us generated based on at least the error value and a dynamic nominal control zone value using a proportional-integral-derivative control algorithm, and the dynamic nominal control zone value is generated in a second control loop based on at least the reference zone rate and the control zone rate. The control zone of the substrate is processed according to the output parameter value.