Apparatus and methods are disclosed for use within an image-guided surgical navigation system for the storage and measurement of trajectories for surgical instruments. An icon representing the real-time trajectory of a tracked instrument is overlaid on one or more pre-acquired images of the patient. At the surgeon's command, the navigation system can store multiple trajectories of the instrument and create a static icon representing each saved trajectory for display. The surgeon may also measure a planar angle between any two trajectories. The angle is computed in the plane of the image, and therefore will be computed separately for each image displayed. Furthermore, the surgeon has the option of computing and displaying the three-dimensional distance between two points defined by any two trajectories.