A method of manufacturing a semiconductor device includes defining a sampling plan in a process control system. Measurement values are obtained at the first number N of the sample points. The first number of measurement values are modelled using a wafer model to generate a first set of coefficients according to a reference model. A second number M of the first number N of sample points is randomly selected. The second number M of measurement values obtained at the second number M of sample points is modelled using the wafer model to generate a second set of coefficients according to a phase_1 model. One of the M sample points is randomly replaced by one of the N−M sample points to obtain a subsample. The measurement values of the subsample are modelled using the wafer model to generate a third set of coefficients according to a phase_2 model.