Building and studying 3D representations of anatomical structures, such as the brain, plays an important role in modern biology and medical science. While 3D imaging methods such as MRI and CT have been widely applied, 2D imaging methods such as optical microscopy typically generate images with much higher resolution. In this thesis I describe how to construct a high-resolution 3D atlas of the mouse brain from 2D microscopic images. In particular, I focus on using computer graphics techniques, such as image registration to correcting tissue distortions and polygonal modeling to build surfaces representing the partitioning of anatomical regions. The methods are being applied to construct a high-quality polygonal atlas of an adult mouse brain from 350 histological tissue sections. While the resulting brain atlas will contribute to a larger project of building a spatial database of gene expressions over the mouse brain, the methods described in this thesis are well suited for the general purpose of building polygonal atlases of arbitrary anatomical structures from tissue sections.