Recent cluster tools can handle diverse wafer flow patterns by changing the logical module configuration. When exceptional events such as module failures, automatic preventive maintenance, or module recoveries, the tool is subject to logical errors such as deadlocks or livelocks. We propose a flexible and systematic procedure of designing an automata-based supervisory control logic for cluster tools to avoid such undesirable behavior and meet the imposed constraints. First, we develop an automata-based model for each possible wafer flow patterns and enforce the predefined constraint rules in automata to remove the undesirable behaviors. Second, we introduce automata models of managing the exceptional cases and overcoming the undesirable behaviors.