Three-dimensional finite element analysis is one of the best ways to assess stress and strain distributions in complex bone structures. However, accuracy in the results may be achieved only when accurate input information is given. A semi-automated method to generate a finite element (FE) model using data retrieved from computed tomography (CT) was developed. Due to its complex and irregular shape, the glenoid part of a left embalmed scapula bone was chosen as working material. CT data were retrieved using a standard clinical CT scanner (Siemens Somatom Plus 2, Siemens AG, Germany). This was done to produce a method that could later be utilized to generate a patient-specific FE model. Different methods of converting Hounsfield unit (HU) values to apparent densities and subsequently to Young's moduli were tested. All the models obtained were loaded using three-dimensional loading conditions taken from literature, corresponding to an arm abduction of 90 degrees. Additional models with different amounts of elements were generated to verify convergence. Direct comparison between the models showed that the best method to convert HU values directly to apparent densities was to use different equations for cancellous and cortical bone. In this study, a reliable method of determining both geometrical data and bone properties from patient CT scans for the semi-automated generation of an FE model is presented.