A plurality of portions of a substrate are monitored during polishing at a first polishing station with an in-situ monitoring system. A plurality of thicknesses are determined based on measurements by the in-situ monitoring system, and the plurality of pressures to apply to the plurality of regions of the substrate are calculated in a closed-loop control system. However, if a representative thickness of the layer is less than a threshold thickness, calculation of the plurality of pressures by the closed-loop control system is halted and a plurality of predetermined pressures are applied to the plurality of regions of the substrate.