The article defines possible requirements for self-regulation (self-organization) of a medical organization implementing regional projects by presenting its static, dynamic and functional prototype models in interaction with physical representation of system. The authors propose a set-theoretical approach for research of specially created prototype models of processes in medical organization that are in objective compliance with actual model implementing regional projects. Formalized processes of prototype models of medical organization (static, dynamic, functional) are classified, studied and visualized. The roles of feedback objects are defined for finding a physical model of prototype implementation, including data (static model), ordering (dynamic model) and methods (functional model), as well as for elaborating various scenarios of system behavior and operability in variable conditions. Project prototypes are selected as structural representations of the project system. Self-organization (self-regulation) is manifested in ability of complex systems to reach a new level of development, resist «entropy» and implement «negentropic» tendencies, adapt to external factors, transforming their structure and maintaining certain stability. Implementation of regional projects will allow acquiring the necessary competencies and processing the results using digital technologies at existing facilities of medical organization. A set-theoretic representation optimizes understanding of the objective and discovers real limitations associated with a tool or approach. Prototyping is effective management product for choice of the best solution from several competing ones.