Several technological applications require acquiring detailed information about the three-dimensional (3D) shape and structure of moving objects. Prominent examples are 3D scanning and 3D microscopy, whose markets are in rapid and evolving expansion. PROCEEDS provides a novel, unified and flexible software framework to retrieve three-dimensional information on complex structures. The software elaborates multiple video-acquisitions - a standard input in most 3D technologies - to produce 3D data of interest. It is based on a powerful tracking algorithm, originally developed to reconstruct 3D individual trajectories of large swarms on the move. By using either actual or virtual tracers in the target object, the software uses the inferred trajectories to characterize the dynamic three-dimensional features of the moving object. The software package has a modular structure, and can be adapted to a variety of different system specific set ups. The Graphical User Interface was implemented using free IT tools to make last-generation cross-platform software easily maintained, upgradeable and running over different operating systems, for best usability both in academic and industry contexts.The software has been tested as a prototypical dynamical 3D scanner in laboratory experiments on deformable rotating bodies, and successfully applied to retrieve local stresses.