1. A computer-based method for localized feature-based wafer surface quantification including the steps of: inputting raw surface geometry data from at least one of a wafer front surface map and a wafer back surface map; defining a region of interest encompassing a localized feature of interest; performing surface fitting to remove low frequency components of said raw surface geometry data in the region of interest to yield a residual image; constructing a two dimensional localized feature metrics (LFM) window encompassing said region of interest; applying said two dimensional LFM window to said residual image to suppress edge and corner artifacts, yielding a window-processed residual image; and processing said window-processed residual image to provide substantially accurate and robust characterization and quantification of said localized feature of interest.