There is a rapidly increasing amount of literature outlining the use of three-dimensional (3D) reconstruction and printing technologies in recent years. However, precise instructive articles which describe step-by-step methods of reconstructing 3D images from computed tomography (CT) or magnetic resonance imaging (MRI) remain limited. To address these issues, this article describes a detailed protocol which will allow the reader to easily perform the 3D reconstruction in their future research, to allow investigation of the appropriate surgical anatomy and allow innovative designs of novel screw fixation techniques or pre-operative surgical planning.