Well-controlled nanostructure of polymer brushes has been fabricated by combining atomic force microscopy (AFM), lithography and surface-initiated polymerization techniques. Self-assembled monolayers (SAMs) of octadecyltrichlorosilane (OTS) were made on silicon surface followed by introduction of nanostructures on these SAMs surface using a conductive AFM tip, where OTS SAMs are oxidized. The oxidized areas are then covered with hydroxyl-terminated silane SAMs, reacted sequentially with 2-bromoisobutyryl bromide to connect initiator groups. Finally, the poly(methyl methacrylate) (PMMA) brushes arrays are formed on this functionalized silicon surface. This technique provides a simple and efficient approach to create various nanostructures of polymer brushes potentially used for designing nanodevices. (C) 2003 Elsevier B.V. All rights reserved.