I believe you need to contact the manufacturer of your machine about the alignment procedure if you are referring to the external optic alignment. Usually on a flying optic system the resonator must be leveled (if not mounted on the frame) or the machine needs to be leveled. The X-Axis alignment must be parallel (up and down/ side to side) which means you may have to do the crosshair or target burns at the near side (by the resonator) and the far side (end of the cutting table).
Again, contact your OEM or check your operation manuals.
