Ion bombardment modification of solid surfaces has long been academic and technological interest. Epi-ready Ge (111) and (100) surfaces were implanted with 40 to 200 keV germanium (Ge), cobalt (Co), and iron (Fe) ions at the dose of 10(15) to 5 x 10(17) ions/cm(2). Cellular nanostructures were observed by scanning probe microscopy (SPM), including scanning tunnelling microscopy (STM), and contact-mode and tapping-mode atomic force microscopy (AFM). These structures are similar (at higher resolution) to those reported in earlier scanning electron microscope (SEM) measurements (I.H. Wilson, J. Appl. Phys., 53 (1982) 1698). In the case of Go-implanted Ge(111), the variation of the root-mean-square roughness (R-q) with ion dose (10(16) to 10(17) ions/cm(2)), accelerating voltage (40 to 70 kV) and mean beam current density (15 to 150 mu A/cm(2)) is presented and explained in terms of ion range and surface temperature. Finally, the effect of the tip shape in the AFM images presented in this paper is discussed.