A 3D measuring instrument and method of operation is provided that includes a registration camera and a an autofocus camera. The method includes capturing with the registration camera a first registration image of a first plurality of points and a first image with the first camera with the instrument in a first pose. A plurality of three-dimensional (3D) coordinates of points are determined based on the first image. A second registration image of a second plurality of points is captured in a second pose and a focal length of the autofocus camera is adjusted. A second surface image is captured with the first camera having the adjusted focal length. A compensation parameter is determined based in part on the captured second surface image. The determined compensation parameter is stored.