Recent advances in optics and electronics have culminated in the development of the laser confocal scanning microscope (LCSM). The LCSM provides unparalleled resolution for localizing fluorescent probes in cells. In combination with advanced, yet relatively inexpensive and compact computers, it is relatively easy to produce 3-dimensional reconstructions of fluorescently labelled structures in cells. We have been working with a state of the art BioRad MRC 600 LCSM with its controlling computer. To produce 3-D reconstructions of data sets obtained with the LCSM we use VoxelView software on a Silicon Graphics Iris Indigo computer. We have used this system for a wide variety of applications, including determining the subcellular distribution of newly defined proteins, following the intracellular trafficking of newly synthesized membrane proteins, studying the migration of developing thymocytes in thymic explants.