An association of a pre-operative plan and tracked position and orientation of a surgical instrument relative patient anatomy in a navigation system is generated. The pre-operative plan includes a virtual representation of the patient anatomy data. Position and orientation of the patient anatomy as well as position and orientation of the surgical instrument within the navigation system is obtained. A virtual representation of the surgical instrument relative the virtual representation of the patient anatomy data is generated in multiple orientations in separate parts of a split window. A system with a tracker comprising a tracker interface for attaching the tracker to the instrument includes a surgical navigation module for generating the virtual representation in a split window.
