Self-assembly of alkanethiol monolayers on gold and silver substrates is a fast, easy, and convenient method for preparing stable organic films with well-defined physical and chemical properties that can be modified by changing the terminal functional group of the molecule. In this correspondence, we report on the use of secondary ion mass spectrometry (SIMS) for characterizing methods of producing micrometer spatial scale patterns of two chemically distinct monolayers on silver and gold surfaces. Production of these molecular patterns is the crucial first step toward the application of monolayer films far biosensor and microelectronic device fabrication. Notably, we found that SIMS has the necessary sensitivity and selectivity to image the distribution of the intact parent molecular ions from each of the monolayers. Thus, SIMS allowed unambiguous confirmation of the correct fabrication of a molecular pattern with micrometer spatial scale resolution.