System and methods for establishing, in combination with an imaging device, a desired orientation of a navigated element having a longitudinal axis, with respect to a bone, the system comprising a jig configured for being directly or indirectly fixed relative to the bone; a positioning head supported by the jig and movable with respect thereto; an angle adjustment member mounted within the positioning head, comprising a passage having a guiding axis, the angle adjustment member being configured for receiving in the passage the navigated element so that the longitudinal axis of the navigated element is aligned with the guiding axis, the angle adjustment member being movable with respect to the positioning head; and an alignment pin having a pin proximal end, a pin distal end and a pin axis, and configured for being received in the passage so that the pin axis is aligned with the guiding axis and so that the pin distal end faces towards the bone, the pin further comprising a light source disposed at its proximal end for projecting an alignment beam along the pin axis in the direction away from the bone for the alignment of the imaging device relative to the guiding axis of the passage for use of the imaging device in establishing the orientation of the guiding axis corresponding to the desired orientation of navigated element.