Super-resolution imaging based on single molecule localization of cellular structures on nanometer scale requires to record a series of wide-field or TIRF images resulting in a considerable recording time (typically of minutes). Therefore, sample drift becomes a critical problem and will lower the imaging precision. Herein we utilized morphological features of the specimen (mammalian cells) itself as reference markers replacing the traditionally used markers (e.g., artificial fiduciary markers, fluorescent beads, or metal nanoparticles) for sample drift compensation. We achieved sub-nanometer localization precision <1.0 nm in lateral direction and <6.0 nm in axial direction, which is well comparable with the precision achieved with the established methods using artificial position markers added to the specimen. Our method does not require complex hardware setup, extra labelling or markers, and has the additional advantage of the absence of photobleaching, which caused precision decrease during the course of super-resolution measurement. The achieved improvement of quality and resolution in reconstructed super-resolution images by application of our drift-correction method is demonstrated by single molecule localization-based super-resolution imaging of F-actin in fixed A549 cells.