We present a generic and efficient chemical patterning method based on local plasma-induced conversion of surface functional groups on self-assembled monolayers (SAMS). Here, spatially controlled plasma exposure is realized by elastomeric poly(dimethylsiloxane) (PDMS) contact masks or channel stamps with feature sizes ranging from nanometer, micrometer, to centimeter. This chemical conversion method has been comprehensively characterized by a set of techniques, including contact angle measurements, X-ray photoelectron spectroscopy (XPS), scanning photoelectron microscopy (SPEM), scanning electron microscopy (SEM), and scanning Kelvin probe microscopy (SKPM). In particular, XPS and SPEM can be used to distinguish regions of different surface functionalities and elucidate the mechanism of plasma-induced chemical conversion. In the case of an octadecyltrichlorosilane (OTS) monolayer, we show that exposure to low-power air plasma causes hydroxylation and oxidation of the methyl terminal group on an OTS-covered Si surface and generates polar functional groups such as hydroxyl, aldehylde, and carboxyl groups, which can allow subsequent grafting of dissimilar SAMS and adsorption of colloid nanoparticles onto the patterned areas with an achievable resolution down to the 50 nm range.