The interface microstructure, based on a (3-mercaptopropyl)trimethoxysilane (HS(CH2)(3)Si(OCH3)(3)) (MPS) self-assembled monolayer, can be controlled by electrochemistry at a gold electrode. The size, number and chemical characteristics of the defect sites can be reproduced. The electrochemically produced defect sizes of the monolayer, at gold electrodes, were calculated based on the change of the electron transfer kinetics. The size of the defects ranged from 15 to 200 Angstrom in diameter. The modified surfaces have been used as a molecular recognition device, even for the same molecules with different oxidation states. The monolayer, with nanometer defects, has potential for use in the study of single molecule electrochemistry.