We have demonstrated that nanostructures of self-assembled monolayer (NSAM) films of alkanethiols can be formed on the GaAs surface of a AlGaAs/GaAs heterojunctions by cleaving the substrates in an octadecylthiol solution diluted with ethanol. NSAMs with line width as narrow as 5 nm were observed by phase imaging using tapping mode cross-sectional atomic force microscopy (TMXAFM). Time dependent observation of the surface in ail revealed that the nanostructual formation occurred as a results of both selective chemisorption of alkanethiol on GaAs surfaces and the oxidation of AlGaAs surface.