Self-assembled monolayers of n-octadecanethiol on Au( 11 1) were studied by scanning tunneling microscopy (STM). The STM images, taken with a high bias (- 1 V) and small (- 1 nA) tunneling current, show self-assembled monolayers with defect sites (pits). Continued scanning in this mode caused small lateral expansion of the pits and eventually a complete morphological change of the n-octadecanethiolcovered surface. Purposeful etching of the self-assembled monolayers could be achieved by bringing the STM probe tip closer to the substrate using a low bias potential (10 mV) and a high tunneling current (10 nA) or by the application of a high bias potential (3 V) for a few seconds. A positive substrate bias (+3 V) pulse always led to pit formation, while a negative (-3 V) substrate bias pulse produced mounds. These mounds could be removed with a positive bias pulse. The modifications induced by potential pulses were attributed to field evaporation of material from substrate or tip material. The atomic structures of etched Au surfaces using an STM tip or strong oxidizing agents, such as chromic acid and peroxide (H2SO4:HzO2 = 7:3) solutions, were remarkably different. The surface structure of the etched area using an STM tip showed complete distortion from the Au(ll1) surface, whereas peroxide solution etching preserved the original Au(ll1) structure.