Characterization techniques available for bulk or thin-film solid-state materials have been extended to substrate-supported nanomaterials, but generally non-quantitatively. This is because the nanomaterial signals are inevitably buried in the signals from the underlying substrate in common reflection-configuration techniques. Here, we propose a data-driven analysis method, inspired by the four-point probe technique for resistance measurement as well as the chop-nod method in infrared astronomy, to characterize nanomaterials without the influence of underlying substrate signals from four interrelated measurements. This method in secondary electron (SE) microscopy, a SE spectrum (white electrons) associated with the reflectivity difference between two different substrates can be tracked and controlled. The SE spectrum is used to quantitatively investigate the covering nanomaterial based on subtle changes in the transmission of the nanomaterial with high efficiency rivaling that of conventional core-level electrons. The method represents a benchmark for surface analysis to provide “free-standing” information about supported nanomaterials.