Nanometer-scale structure of binary thiol self-assembled monolayers (SAMs) prepared by the electrochemical selective replacement of adsorbed thiols in phase-separated binary SAMs has been studied by scanning tunneling microscopy (STM) and cyclic voltammetry. A phase-separated binary SAM of 1-undecanethiol (UDT) and 3-mercaptopropionic acid (MPB) is used as a starting system. MPA, which has a less negative desorption potential, is selectively removed by controlling the electrode potential, and replaced with 1-hexadecanethiol (HDT) or 11-mercaptoundecanoic acid MUA. STM images of the UDT layer remaining after the selective removal of MPA exhibit two types of domains: domains with striped structure and domains where thiol molecules are densely packed, suggesting that some UDT molecules are reoriented and form low-density regions where the molecules are aligned flat on the surface. STM images of UDT-HDT and UDT-MUA binary SAMs formed by the replacement show surfaces which are phase-separated in nanometer scale. The size of the domains after the replacement is approximately equal to that of the initial phase-separated UDT-MPA SAM, indicating that the domain size is not significantly affected by the replacement.