Nanometer scale structures of self-assembled films consisting of 3-mercaptopropionic acid (MPA) were formed by using electric stimuli between scanning tunneling microscope (STM) Au tips and gold surfaces. The obtained structures were compared with those using bare gold surfaces and hexanethiol films on Au(111) under the same conditions. X-ray photoelectron spectroscopy measurements revealed that self-assembled ultrathin films of the corresponding thiol molecules were fabricated on Au(111) by a facile atmospheric-vapor-adsorption (AVA) method without solvent. Comparison of nano-structure formation suggested that the self-assembled thin films of 3-mercatopropionic acid molecules gave nano-dots below the height of voltage pulses where gold atom emission from Au tips and surface evaporation of Au(111) take place. It was found that 3-mercaptopropionic acid films easily produced much better nano-dots on Au(111) than hexanethiol films probably due to the formation of hydrogen bonding networks and/or the reactions of 3-mercaptopropionic acid when electric pulses were applied to the films. (C) 2002 Elsevier Science B.V. All rights reserved.