The authors compare the effects of focused and broad MeV ion beam irradiation on the surface roughness of silicon wafers after subsequent electrochemical anodization. With a focused beam, the roughness increases rapidly for low fluences and then slowly decreases for higher fluences, in contrast to broad beam irradiation where the roughness slowly increases with fluence. This effect is important as it imposes a limitation on the ability to fabricate smooth surfaces using focused ion beam irradiation. For a given fluence, small variations in the resistivity of an irradiated area may arise due to fluctuations of the focused beam current during irradiation. These small variations in resistivity then give rise to an increased roughness during the electrochemical etching. The roughness may be reduced by increasing the scan speed, which alters the way in which the fluctuations in fluence are averaged out over the irradiated surface. (C) 2010 American Vacuum Society. [DOI: 10.1116/1.3406130]