An effective method of system modeling and dynamic scheduling for the back-end line of semiconductor manufacturing is proposed. The virtual factory, describing semiconductor manufacturing line, is designed in detail, and then a Petri net model simulator is developed for operation and control of the modular cells of the virtual factory. The petri net model is a colored timed Petri nets (CTPNs). The simulator will be utilized to analyze and evaluate various dynamic status and operatons of manufacturing environments. The dynamic schedulaer has a hierarchical structure with the higher for planning level and the lower for dynamic scheduling level. The genetic algorithm is applied to extract optimal conditions of the scheduling algorithm. The proposed dynamic scheduling is able to realize the semiconductor manufacturing environments for the diversity of products, the variety of orders by many customers, the flexibility of order change by changing market conditions, the complexity of manufacturing processes, and the uncertainty of manufacturing resources. The proposed method of dynamic scheduling is more effective and useful in dealing with such recent pressing requirements including on-time delivery, quick response, and flexibility.