Swift heavy ions can be used to modify material surfaces on the nanometer scale. In particular, the irradiation of a target surface under grazing angle of incidence offers new possibilities to create chains of individual nanodots with different lengths. The length of these chains can be controlled by the angle of incidence. So far, this method could be successfully applied for insulating materials. The present work dealt with nanosized tracks on the well-known highly oriented pyrolytic graphite surface. By using atomic force microscopy and scanning tunneling microscopy, comparative studies of two different ion beam energies and ion types have been performed. From the analysis of the scanning probe microscopy results, the same track length–angle relation was found, similar to earlier studies on other materials such as SrTiO3.