Stereotactic targeting is a commonly used technique for performing injections in the brains of mice and other animals. The most common method for targeting stereoscopic injections uses the skull indentations bregma and lambda as reference points and is limited in its precision by factors such as skull curvature and individual variation, as well as an incomplete correspondence between skull landmarks and brain locations. In this software tool, a 3D laser scan of the mouse skull is taken in vitro and registered onto a reference skull using a point cloud matching algorithm, and the parameters of the transformation are used to position a glass pipette to place tracer injections. The software was capable of registering sample skulls with less than 100 micron error, and was able to target an injection in a mouse with error of roughly 500 microns. These results indicate that using skull scan registration has the potential to be widely applicable in automating stereotactic targeting of tracer injections.