A system measures the three-dimensional phenotypic characteristics of an animal, such as a dairy cow. The system uses a large number of modulated laser light beams from a lidar camera to measure approximately 100 points per square inch of the animal. Each laser beam measures intensity, horizontal, vertical, and depth dimensions, and by combining the measurements, the system composes a very accurate three-dimensional image of the animal. The systems calculates the desired phenotypic measurements for conformation of the animal by combining measurements of selected points on the animal. The system then stores the measurements for each animal in a computer data base for later use. The system also stores a light intensity image of the animal's markings which is compared to other stored images.