This article describes the processing of computed tomography (CT) images with MATLAB for the fabrication of anatomically correct head phantoms. Such phantoms are applied for the verification of systems for image-guided interventions. For this purpose, a CT-image set of a patient's head has been read into MATLAB and the skin part (soft tissue between head and bone surface) and some bone parts were segmented separately. A number of positioning and connection elements were generated in both skin and bone parts for later assembly of the phantom. Finally, the segmented skin and bone parts have been converted into Stereolithography format (STL) for printing with a 3D printer. The complete process was successfully tested with a patient individual CT data set. Moreover, the accuracy of the added positioning and connection elements was measured. The preliminary results show that this MATLAB-based module is suitable for processing of CT image data for the fabrication of realistic anatomical phantoms.