With the increasing number of medical programs, research for new teaching methods has also emerged. Computer software and diagnostic images have been used for anatomy teaching as an alternative to cadaver dissection, which means students cannot develop a mental image of the human body without compromising spatial reasoning. Also the cadavers present flaws such as color, texture and smell. This paper explains in details the protocol used to reconstruct 3D models for rapid prototyping as an overcome to these difficulties. Online Computerized Tomography scans were obtained in DICOM format from OsiriX and InVesalius. Reconstruction of 3D models from aortic and superior tracheobronchial tract structures were created, InVesalius and Rhinoceros software were used. 3D models of a heart with its aorta, superior tracheobronchial tract and an aneurysm at the aortic bifurcation were obtained for rapid prototyping. The superior tracheobronchial tract model was printed. It is possible to produce printed models from CT scans using different softwares for 3D modeling and rapid prototyping. These models could allow the student to develop a three dimensional mental image of the human body according to literature.