A system and method of controlling multi-process, multi-product semiconductor fabrication tools. Individual, grouped, or composite controllers are designated to control various tool operations. First control parameters for a fabrication tool process are generated, where the first control parameters are based on first tool operation attributes. Second control parameters for the process are generated based on second tool operation attributes. The fabrication tool is then controlled by generating cooperative control parameters which are a function of the first and second control parameters. Disturbance information can be shared between controllers for use in generating the first and second control parameters while taking into account disturbance information already discovered and quantified.