A method and system for estimating context offsets for run-to-run control in a semiconductor fabrication facility is described. In one embodiment, contexts associated with a process are identified. The process has one or more threads, and each thread involves one or more contexts. A set of input-output equations describing the process is defined. Each input-output equation corresponds to a thread and includes a thread offset expressed as a summation of individual context offsets. A state-space model is created that describes an evolution of the process using the set of input-output equations. The state-space model allows to estimate individual context offsets.