A surgical system, method and CAD program are provided. The surgical system includes a digitization device including a pointer tip to contact a target site and actuatable control input(s). A surgical tool can manipulate the target site. A navigation system tracks a state of the digitization device. Controller(s) receive the tracked state of the digitization device and display, within a virtual reference frame, a virtual representation of the pointer tip. In response to actuation of the control input(s), the controller(s) register virtual reference points within the virtual reference frame based on the pose of the virtual representation of the pointer tip and enable arrangement of one or more geometrical design objects within the virtual reference frame relative to the registered virtual reference points to generate a virtual boundary that defines a region of the target site to be avoided by the surgical tool.