Focused ion beam techniques are among the most important tools for the nanostructuring of surfaces. As the physical phenomena during milling are not fully understood yet, we have applied the phase imaging capabilities of tapping mode atomic force microscopy to the investigation of surface amorphization, sputtering, and redeposition caused by, focused ion beam irradiation. We have performed single spot as well as large area (20 X 20 mum(2)) irradiation of silicon (100) wafers. We describe the localized formation of amorphous and electrostatically charged domains, which do not correlate to topographic features. (C) 2003 American Vacuum Society.