Due to dramatic advances in optical microscope technology, it is now possible to examine biological specimens in three-dimensions with either electron microscopy or light microscopy. Although the algorithms used for generating the three-dimensional reconstructions are well known, much work remains on developing methods for the display and analysis of the resultant complicated three-dimensional data. In the first part of this paper, we will introduce image processing schemes for enhancing features in data and some computational methods for manipulating three dimensional data sets. In the second part, we will discuss the image display system in the context of software design and hardware requirements, which must be considered for convenient data visualization and measurement. Much effort has been spent on developing a generalized display system that can also be used for model building and analysis. By model building we mean the interactive tracking of features in three-dimensional volumetric images. Throughout this chapter we will make a distinction between display methods that directly utilize three-dimensional image data stored as a contiguous set of pixels (also called volumetric data, or voxel data) and those that convert the data into a set of polygon vertices that define a single-level contour surface. Although this latter approach contains much less information than volumetric approaches, it can make stunning pictures. Figure 1 shows a typical procedure for handling three-dimensional data involving image enhancement, data manipulation, data display and analysis.