Three-dimensional (3D) reconstruction and finite element analysis (FEA) have been extensively used to simulate cervical biomechanics. However, instructive articles providing full descriptions for operating Mimics software, Geomagic software, and FEA are rare in the literature. This omission has hindered research and development related to cervical spine biomechanics. Herein, we expound a detailed and easily understandable protocol for performing a digital biomechanics study which may facilitate a better understanding of the internal anatomy mechanics and the investigation of novel screw fixation techniques. We describe step-by-step instructions for use of Mimics and Geomagic software in FEA, along with a concise literature review. The key procedures of digital FEA stepwise instruction are presented, accompanied by a brief but complete report on the computed tomography (CT) imaging data for establishing the final finite element model. Previous publications regarding the commonly used software are also reviewed and discussed. Each piece of software performs a specific function for digital FEA establishment and each has its inherent shortcomings, making it is necessary to combine the software to leverage the advantages of each in order to best serve finite element research. For reasons of brevity, this study only provides an illustrative report on a small key part of finite element research in the cervical spine. These stepwise instructions can guide orthopedic researchers in conducting FEA studies in digital cervical biomechanics.