A method of generating a matrix to relate a plurality of controllable parameters of a chemical mechanical polishing system to a polishing rate profile includes polishing a test substrate. The test substrate is polished for a first period of time using baseline parameter values with a first parameter set to a first value, and the test substrate is polished for a second period of time using first modified parameter values with the first parameter set to a modified second value. A thickness of the test substrate is monitored during polishing, and a baseline polishing rate profile is determined for the first period of time and a first modified polishing rate profile is determined for the second period of time. The matrix is calculated based on the baseline parameter values, the first modified parameters, the baseline polishing rate profile and the first modified polishing rate profile.
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