A method, system, and program product are provided for removing artifacts from an EM field generator from a rotational 3D scan. The method comprises: preoperatively, characterizing the artifacts from the EM field generator over a range of rotational positions of an x-ray source and detector intraoperatively, determining the position of the EM field generator relative to the x-ray source and detector and removing the preoperatively characterized artifacts for the determined relative position of the EM field generator from current x-ray image.