A physician preparing to perform a surgical procedure may view pre-operative images of a procedure area of a patient and use a stylus or other interface to draw boundaries between or around areas shown in the images that should be treated with extreme caution during the procedure. These boundaries may be provided by an image guided surgery navigation system and used to provide warnings (e.g., audible or visual alerts having characteristics associated with the proximity to the bounded area) and control operations of a medical instrument (e.g., reducing a cutting speed or disabling the medical instrument entirely) during the procedure in order to reduce risks associated with using the medical instrument in or around the bounded areas. Other safety features that may be defined or pre-configured based on the procedure include reacting to movement patterns (e.g., high linear speed) and location patterns (e.g., steady advancement towards an unsafe area).
