Kinetic Monte Carlo (KMC) is regarded as an efficient tool for rare event simulation and has been applied in simulating bottom–up self-assembly processes of nanomanufacturing. Yet it has limitations to simulate top–down processes. In this paper, a new and generalized KMC mechanism, called controlled KMC or controlled KMC (cKMC), is proposed to simulate complete physical and chemical processes. This generalization is enabled by the introduction of controlled events. In contrast to the traditional self-assembly events in KMC, controlled events occur at certain times, locations, or directions, which allows all events to be modeled. A formal model of cKMC is also presented to show the generalization. The applications of cKMC to several top–down and bottom–up processes are demonstrated.