Disclosed are methods and apparatus for measuring a characteristics of a through-silicon via (TSV) structure. A beam profile reflectivity (BPR) tool is used to move to a first xy position having a TSV structure. The BPR tool is then used to obtain an optimum focus of at the first xy position by adjusting the z position to a first optimum z position for obtaining measurements at the first xy position. Via the BPR tool, reflectivity measurements for a plurality of angles of incidence are obtained at the first xy position. One or more film thicknesses for the TSV structure are determined based on the reflectivity measurements. A z position can also be recorded and used to determine a height of such TSV structure, as well as one or more adjacent xy positions.