Technological processes of biocompatible components are of utmost importance when making implants and reconstruction of anatomical geometry. The fast technological progress has enabled closer cooperation between researchers in the field of biotechnology. Existing protocols and solutions must be constantly developed and frequently changed, taking into account the existing structure which are to be adapted to the trends and everyday challenges. Therefore, the paper provides a comprehensive theoretical view of the technology of additive manufacturing systems, medical diagnostics, segmentational techniques and analyses of existing protocols during the reconstruction of anatomical geometry. The aim of this thesis was to optimize the technological process of manufacturing biocompatible parts which are to be reconstructed and also of implants which are to be developed while respecting the right of every patient for the best service and medical care. For this purpose, an analysis of existing technologies and protocols have been used and defined by new guidelines and with a new protocol, taking into account the available technological capabilities, their limitations and advantages. Finally, a review of several case studies with a detailed presentation based on the use of techniques has been described. Clearly, for the purposes of this dissertation, new protocols and software solutions have been developed.