Using a scanning probe lithography method known as nanografting in conjunction with knowledge of self-assembly chemistry, regulation of the heterogeneity of self-assembled monolayers ( SAMs) is demonstrated. While nanografting in single-component thiols produces areas of SAMs with designed geometry and size, nanofabrication in mixed thiol solution yields segregated domains. The reaction mechanism in nanografting differs significantly from self-assembly in mix-and-grow methods, as proven in systematic studies reported in this article and a companion paper of theoretical calculations of the nanografting process. Knowledge of the reaction pathways enables development of methods for shifting the interplay between the kinetics and thermodynamics in SAM formation, and thus the heterogeneity of mixed SAMs. By varying fabrication parameters, such as shaving speed, and reaction conditions, such as concentration and ratio of the components, the lateral heterogeneity can be adjusted ranging from near molecular mixing to segregated domains of several to tens of nanometers.