Trajectory frame assemblies for image guided surgical systems have a trajectory frame with a support column that can removably secure different components such as a tracking probe and an MER driver adapter to define and/or follow a desired intrabody trajectory. The trajectory frame assemblies include fins attached to the column support and a platform optionally with an X-Y table and/or arcuate reference brackets that are attached to the trajectory frame assemblies and can hold a reference frame with fiducials.