A method of controlling polishing includes polishing a first substrate having an overlying layer on an underlying layer or layer structure. During polishing, the substrate is monitored with an in-situ monitoring system to generate a sequence of measurements. The measurements are sorted into groups, each group associated with a different zone of a plurality of zones on the substrate. For each zone, a time at which the overlying layer is cleared is determined based on the measurements from the associated group. At least one second adjusted polishing pressure for at least zone is calculated based on a pressure applied in the at least one zone during polishing the substrate, the time for the at least one zone, and the time for another zone. A second substrate is polished using the at least one adjusted polishing pressure.