In this study, the effect of the geometrical configuration of retroreflective markers on the maximum tracking uncertainty of target points during a medical navigation is analyzed. Methods that help users select and set up an optimal configuration for minimizing the navigation uncertainty are proposed. The methods are evaluated by simulating surgical navigation environment using an optical tracking system. The result shows that the maximum uncertainty of tracking the target points lying outside the marker region is a function of the configuration of some of the associated markers and the precision of the optical tracking system used. We also show that the use of flexible rigid bodies minimizes target tracking uncertainty by enabling a customized reconfiguration of markers for optimal pose with respect to individual surgical target position during preoperative planning phase.