A 3D measuring instrument includes a registration camera and a surface measuring system having a projector and autofocus camera. In a first pose, the registration camera captures a first registration image of first registration points. The autofocus camera captures a first surface image of first light projected onto the object by the projector and determines first 3D coordinates of points on the object. In a second pose, the registration camera captures a second registration image of second registration points. The autofocus camera adjusts the autofocus mechanism based at least in part on adjusting a focal length to reduce a difference between positions of the first and second registration points. A second surface image of second light is captured. A compensation parameter is determined based at least in part on the first registration image, the second registration image, the first 3D coordinates, the second surface image, and the projected second light.