A system and method for analyzing a three-dimensional structure of a sample includes generating a first x-ray beam having a first energy bandwidth less than 20 eV at full-width-at-half maximum and a first mean x-ray energy that is in a range of 1 eV to 1 keV higher than an absorption edge energy of a first atomic element of interest, and that is collimated to have a collimation angular range less than 7 mrad in at least one direction perpendicular to a propagation direction of the first x-ray beam; irradiating the sample with the first x-ray beam at a plurality of incidence angles relative to a substantially flat surface of the sample, the incidence angles of the plurality of incidence angles in a range of 3 mrad to 400 mrad; and simultaneously detecting a reflected portion of the first x-ray beam from the sample and detecting x-ray fluorescence x-rays and/or photoelectrons from the sample.