We present a preprocessing and segmentation scheme designed to address the particular difficulties encountered in the analysis of magnetic resonance cholangiopancreatography (MRCP) data, as a precursor to the application of computer assisted diagnosis (CAD) techniques. MRCP generates noisy, low resolution, non-isometric data which often exhibits significant greylevel inhomogeneities. This combination of characteristics results in data volumes in which reliable segmentation and analysis are difficult to achieve. In this paper we describe a data processing approach developed to overcome these difficulties and allow for the effective application of automated CAD procedures in the analysis of the biliary tree and pancreatic duct in MRCP examinations.