A method of analyzing a sample with a probe based measurement instrument using stiffness tomography. Stiffness or elastic modulus data obtained through contact measurement with the sample as a function of depth is used in the detection of features, particularly subsurface features, based on stiffness or elastic modulus differential. In an AFM, a probe tip is indented, preferably until it reaches a desired depth, and force-deflection data is measured as a function of depth. The FD data is broken into subsets or segments, each of which is independently analyzed to determine a stiffness or elastic modulus. The stiffness or elastic modulus data is used in determining whether there is great enough difference or contrast in any portion of the data to detect presence of a feature with a stiffness different than its surroundings. Such data can be imaged and/or manipulated to provide an image of subsurface features.