A series of nanoscale chemical patterning methods based on soft and hybrid nanolithographies have been characterized using scanning electron microscopy with corroborating evidence from scanning tunneling microscopy and lateral force microscopy. We demonstrate and discuss the unique advantages of the scanning electron microscope as an analytical tool to image chemical patterns of molecules highly diluted within a host self-assembled monolayer and to distinguish regions of differential mass coverage in patterned self-assembled monolayers. We show that the relative contrast of self-assembled monolayer patterns in scanning electron micrographs depends on the operating primary electron beam voltage, monolayer composition, and monolayer order, suggesting that secondary electron emission and scattering can be used to elucidate chemical patterns.