An improved system and method for macroscopic and microscopic surgical navigation and visualization are presented. In exemplary embodiments of the present invention an integrated system can include a computer which has stored three dimensional representations of a patient's internal anatomy, a display, a probe and an operation microscope. In exemplary embodiments of the present invention reference markers can be attached to the probe and the microscope, and the system can also include a tracking system which can track the 3D position and orientation of each of the probe and microscope. In exemplary embodiments of the present invention a system can include means for detecting changes in the imaging parameters of the microscope, such as, for example, magnification and focus, which occur as a result of user adjustment and operation of the microscope. The microscope can have, for example, a focal point position relative to the markers attached to the microscope and can, for example, be calibrated in the full range of microscope focus. In exemplary embodiments of the present invention, the position of the microscope can be obtained from the tracking data regarding the microscope and the focus can be obtained from, for example, a sensor integrated with the microscope. Additionally, a tip position of the probe can also be obtained from the tracking data of the reference markers on the probe, and means can be provided for registration of virtual representations of patient anatomical data with real images from one or more cameras on each of the probe and the microscope. In exemplary embodiments of the present invention visualization and navigation can be provided by each of the microscope and the probe, and when both are active the system can intelligently display a microscopic or a macroscopic (probe based) augmented image according to defined rules.