An electromagnetic intramedullary nail screw positioning system is used to assist an orthopaedic surgeon to correctly aligned a screw drill guide with a screw receiving aperture in an intramedullary nail during surgery. However due to the large number of different types of intramedullary nail, the system must be calibrated during each surgery. An improved calibration system is described that no longer requires the surgeon to perform the calibration during the surgery in order to save time and improve robustness. The system is periodically calibrated and a memory stores offset information for a range of nails types relative to a reference nail. During surgery, the surgeon enters a nail identifier, and the system looks up the associated offset and applies this offset to the measured signals to guide alignment of the screw drill guide with the screw receiving aperture.