We have observed surface chemical reactions which occur at the impact sites on a Si(1 1 1)-(7 × 7) surface and a highly oriented pyrolytic graphite (HOPG) surface bombarded by highly charged ions (HCIs) by using a scanning tunneling microscope (STM). Crater structures are formed on the Si(1 1 1)-(7 × 7) surface by single I50+-impacts. STM-observation for the early step of oxidation on the surface suggests that the impact site is so active that dangling bonds created by HCI impacts are immediately quenched by reaction with residual gas molecules. We show also the selective adsorption of organic molecules at a HCI-induced impact site on the HOPG surface.