The navigation systems and methods facilitate aligning a tool in relation to a trajectory in real-time to receive input data from a pre-operative plan image, at least one multi-modal image, and at least one real-time multi-modal image; interactively track at least one neural fiber, whereby interactively tracked fiber data is obtainable; automatically generate output data by way of data transformation using the input data and the interactively tracked neural fiber data; and transmit the output data to at least one of: at least one display device for rendering at least one real-time interactive navigation display for facilitating neural navigation, and at least one drive device for positioning at least one tracking device in relation to the tool in real-time, whereby real-time alignment data is achievable, and whereby at least one neurological structure is preservable.