Laser trackers have been developed that project laser beams and use optical systems to provide three dimensional coordinate measurements. The laser trackers incorporate a servo system to steer a laser beam so that it tracks a retro-reflector, such as a corner cube. The line of sight gimbal angles and the radial distance to the retroreflector are used to determine the coordinates of the retroreflector relative to the tracker. In this paper, we explore the use of the laser tracker to define the metrology for aligning optical systems, including the use of mirrors and windows. We discuss how to optimize the geometry to take advantage of the tracker's most accurate measurements. We show how to use the tracker for measuring angles as well as points.