A confocal image processing system is developed for automatic identification (recognition) and characterization of confocal fluorescent images (serial optical sections). The system is capable of identifying a large percentage of structures (e.g., DNA replication sites) in the presence of background noise and non specific staining of cellular structures. A combination of image processing techniques are applied to successively refine the input image and is so organized as to find the surfaces of highly visible structures first, using simple image processing techniques, and then to adjust and fill in the missing areas of these object surfaces using a number of more complex image processing techniques. As a result, the image analysis system is capable of obtaining morphometric parameters such as surface area, volume, and position of structures of interest automatically. The system provides a powerful tool for biomedical research such as micro-structure characterization, morphogenesis, cell differentiation, tissue organization, and embryo development. We illustrate the performance of the confocal image analysis system by using an image of DNA replication sites in a mammalian 3T3 cell.