Systems, methods and apparatus register a bone for milling during a procedure. A surgeon mills the bone without first performing an explicit registration of a tool relative to the bone. Tool location measurements in combination with a 3-dimensional (3D) model of the patient's bone, such as a segmented CT scan, are used to automatically construct a registration. The 3D model identifies a border where cancellous bone within the bone ends and the cortical bone begins at an inner cortical bone surface. Responsive to movement of the tool within the bone along an initial trajectory, and, using a localizing system to identify the location of tool when in contact with the inner cortical bone surface, a shape/map of the cortical bone is generated and fit to the 3D model automatically to obtain a registration. An updated trajectory may be output such as from 3D implant plan information to guide further milling.