A quantitative surface reconstruction technique has been developed for the geometric characterization of three-dimensional structures by using a combined focused ion beam-scanning electron microscopy (FIB-SEM) instrument. A regular pattern of lines is milled at normal incidence on the sample to be characterized and an image is acquired at a large tilt angle. By analyzing the pattern under the tilted view, a quantitative estimation of surface heights is obtained. The technique has been applied to a test sample and nanoscale resolution has been achieved. The reported results are validated by a comparison with atomic force microscopy measurements.