Computer aided fixture design (CAFD) allows engineers to prototype quickly; however, it does not yet provide a reliable prediction of the system's dynamic behavior. A desired design could be intelligent fixture, with the challenge being to make it even smarter. Thus, this research aimed to identify factors that affect the dynamic behavior of the workpiece-fixture system, and therefore need to be integrated into simulation models. The effects of factors such as locator positions, clamping force, clamping sequence, and others were studied. Results showed that the position of the fixture elements has the largest effect on system dynamics behavior. Selecting the optimum positions ensures a higher natural frequency while also it determines the optimal clamping force and points. Based on these results, CAFD models should consider the dynamic behavior during planning and allow testing it in the verification stage.