Methods and systems for selecting wafer locations to characterize cross-wafer variations based on high-throughput measurement signals

Methods and systems for selecting measurement locations on a wafer for subsequent detailed measurements employed to characterize the entire wafer are described herein. High throughput measurements are performed at a relatively large number of measurement sites on a wafer. The measurement signals are transformed to a new mathematical basis and reduced to a significantly smaller dimension in the new basis. A set of representative measurement sites is selected based on analyzing variation of the high throughput measurement signals. In some embodiments, the spectra are subdivided into a set of different groups. The spectra are grouped together to minimize variance within each group. Furthermore, a die location is selected that is representative of the variance exhibited by the die in each group. A spectrum of a measurement site and corresponding wafer location is selected to correspond most closely to the center point of each cluster.