Epi-ready Ge(111) surfaces were implanted with cobalt ions to doses of1016–5×1017ions/cm2at accelerating voltages of 40–70 kV. Cellular nanostructures were observed by contact mode and tapping mode atomic force microscopy (AFM). These are similar (at higher resolution) to those reported in earlier scanning electron microscope measurements. Image distortions observed in contact mode AFM are attributed to not only the effect of the tip size but also the change of the effective tip shape due to the softness and stickiness of the implanted surface layer. The variation of the root-mean-square roughness with ion dose (1016–1017ions/cm2), accelerating voltage (40– 70 kV), and mean beam current density (15–150μA/cm2)is presented and explained in terms of ion range and surface temperature.