A plurality of autonomous control processes, with each controlling one or more components of the material transport (or processing) system, is used to radically simplify the controller software. Each autonomous control process is responsible for the actions of only a subset of the cluster tool components. For example, in one embodiment, a separate autonomous control process is used to control each automated component in the material handling system. However, other embodiments in which a control process controls a plurality of components are also contemplated.The control processes can also be implemented as rules-based machines, determining the proper action based on a set of fixed or programmable rules. Alternatively, the control processes may also execute traditional software algorithms. The control processes are designed such that, together they achieve the process flow and throughput requirements previously achieved via a single control process.