The objective of this paper is to introduce a Petri net-based modeling structure with a state space representation for manufacturing systems within the context of hierarchical control. A Flexible Manufacturing Cell (FMC) having parallel processing capability and a material handling system with limited capability is investigated. A machine-oriented timed colored Petri net (TCPN) modeling technique is introduced to represent both sequential and parallel processes characteristics of the cell. Based on a TCPN model at the cell level, a workstation level model is configured through a top-down decomposition approach resulting in a hierarchical multilevel PN model. The dynamical system representation of the TCPN model at the cell level is transformed into a mathematically based state space model. The control for the FMC is formulated within a discrete-time optimal control framework with varying time intervals and a time-variant state equation. A scheduling heuristic solution and associated performance evaluation results are discussed. The state space representation at the workstation level is also discussed to demonstrate the continuity of the proposed modeling structure.