A sophisticated experiment requiring multiple micrometer-scale scanning of the same area of a sample may be performed easily if special positioning features on the surface are available. A set of nanomarkers developed using a nanoscratching technique can provide an efficient, submicron-accurate solution allowing us to investigate various phenomena. In this paper, the analysis of the roughness estimation repeatability is presented in terms of defining the accuracy of the area of interest. The obtained results confirmed the possibility of the repeatable positioning of the sample in an atomic force microscope, providing area roughness determination repeatability with a standard distribution smaller than 3%. As an example, the observation of light-caused surface degradation is presented. Also, the utilization of nanomarkers in determining the magnetic domain's rearrangement angle with an accuracy better than 0.5° is shown.