An accurate method for the characterization of the topographic evolution of materials during dissolution at the submicrometric scale is reported. This method is based on the recording of Environmental SEM tilted images of a selected zone at the surface of a sample for various dissolution times. After each observation, a 3D surface reconstruction was made leading to a series of height maps of the selected zone of interest. One 3D reconstruction was compared to an AFM image of the same zone in order to estimate the accuracy of the heights determined using stereoscopic images. The maximum achievable resolution along the z-axis on the 3D reconstructions was found to be 38 nm. Several micro-structural parameters were extracted from the 3D-image series and their evolutions were related to the dissolution process. This method offers new insights for the monitoring of the changes occurring at the surface of a sample at the micrometer scale during dissolution or corrosion of the material.