An AutoMod simulation model was constructed for real-world 4.5th-generation (4.5G) Thin Film Transistor - Liquid Crystal Display (TFT-LCD) Color Filter (CF) fabrication plants in this study. The characteristics and data of customer orders, production facility, material handling tools, and warehouse (also called stocker) were collected from real plants. Based on these, a simulation model was developed and validated. As the simulation model was complex and had different parameters representing the operation details in the plants, it is of interest to justify the effects of these parameters to the key performance indicators such as system throughput and equipment utilization. Using fishbone analysis, sensitivity analysis and experimental design, a series of simulation experiments were conducted and the resulting simulation model was representative to the CF plants. On the basis of the simulation model with 3-dimension animation, decision makers can conduct what-if analysis for the evaluation of production control policies such as in-process capacity and tact time without disturbing the operations in the real plant. Better alternatives leading to higher system throughput can be identified in system simulation before its real implementation in the fab.