Field-emission electron microscopy (FE-SEM) was applied to observe coplanar microstructures composed of two different types of organosilane self-assembled monolayers (SAMs). These binary microstructures were prepared on silicon substrates covered with native oxide by a lithographic technique. Four types of organosilane precursors, they are n-octadecyltrimethoxysilane (ODS), heptadecafluoro-1,1,2,2-tetrahydro-decyl-1-trimethoxysilane (a type of fluoroalkylsilane, FAS), n-(6-aminohexyl)aminopropyltrimethoxysilane (AHAPS), and 4-(chloromethyl)phenyltrimethoxysilane (CMPhS), were used in this study. Micropatterns composed of the SAMs were clearly imaged by FE-SEM at low acceleration voltages, around 0.6 kV. The brightness order of the SAMs in FE-SEM was ODS > AHAPS > CMPhS > FAS. Through ab initio molecular orbital calculations, the origin of this FE-SEM contrast was ascribed to the electron affinity between the SAMs, which governed the FE-SEM image contrast. It has been successfully demonstrated that FE-SEM could provide us chemical information on organic films with a monomolecular thickness on a solid support.