A surgical navigation system and method for identifying positions on a patient, including a processor, and a tracking system for tracking a pointer tool. The processor is programmed to initialize a surface trace acquisition, continuously record the positions of the pointer tool during the surface, conduct trace acquisition, combine the positions recorded during the surface trace acquisition into a surface trace, receive a patient image of the patient, extract a surface from the patient image, compute a registration transform between the surface traces and the surface for patient registration, segment the patient image into a regions where each region contains an anatomical landmark, determine a spatial distribution of surface traces among the regions; determine whether the spatial distribution in relation to each region minimizes deviance below a threshold, and if the determination is exceeding the threshold, provide information relating to such region.