The scanning tunneling microscope (STM) is employed to monitor the effect of adsorption of an n-alkanethiolate monolayer, from an aqueous solution of the thiol, on the apparent topography of nanoscopic silver adsorption sites. Silver nanodisk structures, 1000-1500 Angstrom in diameter and 50- 150 A in height, were electrochemically deposited on graphite surfaces by using the STM. The topography of these adsorption sites was then determined in situ by STM imaging prior to the exposure of the nanostructure to an aqueous solution of an n-alkanethiol. Immediately following exposure to the thiol, STM images revealed an increase in the height of the nanostructure resulting from the self-assembly of an n-alkanethiolate monolayer on the silver surface. The apparent thickness of the self-assembled monolayer (SAM), estimated from the difference in the nanostructure height measured before and after adsorption of the monolayer, increased linearly with the alkyl chain length for five n-alkanethiols (i.e., CnH(2n+1)SH) having even-numbered chain lengths from n = 10 to 18. For SAMs of tetradecanethiol (CH3(CH2)(13)SH), hexadecanethiol (CH3(CH2)(15)SH), and octadecanethiol (CH3(CH2)(17)SH), the average height increments (20, 24, and 28 Angstrom, respectively) equaled the expected all-trans chain length of these molecules within the experimental precision of our measurement, indicating that little penetration of the STM tip into the surface of the monolayer occurs during the STM imaging experiment.