The aim of this paper is to give a practical overview, showing how recent available digital technology can be combined to build a laboratory capable to produce 3D (and reproduce in 3D) anatomical models for research, teaching and museum exhibitions on topics related to anatomy, morphology in natural sciences, biology and medicine. We present workflows in our Virtual Morphology Lab that can be used for research, training (museum, academic), and external service. We first review different surface scanning equipment and post-processing techniques that are useful for scanning in museum collections and provide technical recommendations for hard- and software as well as storing media on the web. This section is followed by an overview of available software packages for rigorous and effective 3D measurements of landmarks and sliding semi-landmarks, providing extensive supplementary information with guiding manuals for self-teaching in these cutting-edge but complicated research methods. We review briefly most recent work on virtual GM and describe ways for representing results in form of 3D images and 3D prints (outputs). The last part is dedicated to a summary of our experience in 3D-printing using FDM technology of differently sized printers and thermoplastic materials. Finally, we discuss the above-described workflows and its potential applications in research (paleo, biomedical), teaching and museums pedagogics.