A method of generating a matrix for associating 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 using baseline parameter values having the first parameter set to a first value, and the test substrate is polished using the first modified parameter values having the first parameter set to a second modified value. polished during the second period. The thickness of the test substrate is monitored during polishing, a baseline polishing rate profile is determined for a first time period, and a first modified polishing rate profile is determined for a second time period. 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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