Polishing with measurement prior to deposition of outer layer

A computer program product, encoded on one or more non-transitory computer storage media, comprising instructions that when executed by one or more computers cause the one or more computers to perform operations comprising:

• storing a base measurement, the base measurement being a measurement of a substrate after deposition of at least one layer overlying a semiconductor wafer and before deposition of an outer layer over the at least one layer;
• after deposition of the outer layer over the at least one layer and during polishing of the outer layer on substrate by a polishing system, receiving a sequence of raw measurements of the substrate from an in-situ monitoring system;
• normalizing each raw measurement in the sequence of raw measurement to generate a sequence of normalized measurements using the raw measurement and the base measurement;
• determining at least one of a polishing endpoint or an adjustment for a polishing rate based on at least the sequence of normalized measurements;
• and
• at least one of causing the polishing system to halt polishing at the polishing endpoint or causing the polishing system to adjust the polishing rate by the adjustment.