1. A method of obtaining nanotopographic data for a substrate, comprising: measuring a height profile across an entire surface of the substrate to obtain a measured data set; and high pass filtering the measured data set, said high pass filtering comprising, fitting the measured data set to a preset function and producing a flattened data set by taking a difference between the measured data set and the fitted data set, adaptive filtering the flattened data set to produce an adaptive filtered data set, and multiplying the adaptive filtered data set by a masking function that is a fixed non-zero value when the adaptive filtered data corresponds to a location within the measured data set and is zero when the adaptive filtered data corresponds to a location outside the measured data set.