This paper presents a framework for extracting surface models from a broad variety of volume datasets. These datasets are produced from standard 3D imaging devices, and are all noisy samplings of complex biological structures with boundaries that have low and often varying contrasts. The level set segmentation method, which is well documented in the literature, creates a new volume from the input data by solving an initial value partial differential equation (PDE) with user-defined feature-extracting terms. However, level set deformations alone are not sufficient, they must be combined with powerful initialization techniques in order to produce successful segmentations. Our level set segmentation approach consists of defining a set of suitable pre-processing techniques for initialization and selecting/tuning different feature-extracting terms in the level set algorithm. This collection of techniques forms a toolkit that can be applied, under the guidance of a user, to segment a variety of volumetric data.