The difficulties traditionally faced by functional morphologists in representing and interpreting three-dimensional objects can now be mostly overcome using available laser and computer imaging technologies. A practical method for three-dimensional imaging of small mammalian teeth using confocal microscopy is reported. Moulding and casting of the teeth were first performed, followed by confocal fluorescence imaging. Accuracy and precision of the scanned structures were tested in morphometric studies by using a new technique to measure the noise in the scan of a three-dimensional surface, and linear and angular dimensions of the scans were compared with measurements made using traditional morphological tools. It is shown that measurements can be taken with less than 4% difference from the original object. Teeth of the microchiropteran bat Chalinolobus gouldii were scanned and measured to show the potential of the techniques. Methods for visualizing the small teeth in three-dimensional space, and animating the teeth in occlusion, show the power of this approach in aiding a three-dimensional understanding of the structure and function of teeth and other three-dimensional structures.