Summary. We present a set of coherent methods for the nearly automatic creation of 3D geometric models from large stacks of images of histological sections. Threedimensional surface models facilitate the visual analysis of 3D anatomy. They also form a basis for standardized anatomical atlases that allow researchers to integrate, accumulate and associate heterogeneous experimental information, like functional or gene-expression data, with spatial or even spatio-temporal reference. Models are created by performing the following steps: image stitching, slice alignment, elastic registration, image segmentation and surface reconstruction. The proposed methods are to a large extent automatic and robust against inevitably occurring imaging artifacts. The option of interactive control at most stages of the modeling process complements automatic methods.