Additive manufacturing technologies rely on extensive digital data processing, beginning with 3D-CAD model development and continuing through data preparation, process planning, manufacturing execution, and post-processing operations. As additive manufacturing systems become increasingly adopted in aerospace, space, defense, and other critical industrial sectors, ensuring the security of both digital and physical assets becomes a significant challenge. This paper presents a multi-layer cyber-physical security framework for additive manufacturing environments. The proposed approach distinguishes three complementary security layers: the 3D geometric data processing layer, the technological process data layer, and the physical process layer. For each layer, critical assets, potential cybersecurity threats, and recommended protection mechanisms are identified and analyzed. Particular attention is devoted to the protection of engineering data, process parameters, machine configurations, simulation results, and manufacturing infrastructure, as these elements directly influence the quality, reliability, and operational safety of manufactured components. The paper further extends the analysis by introducing a multi-level physical protection model dedicated to additive manufacturing facilities and evaluating the proposed security measures using the Confidentiality–Integrity–Availability (CIA) model. The results demonstrate that effective protection of additive manufacturing environments requires the integration of organizational, physical, and cyber-physical security mechanisms across the entire production lifecycle. The proposed framework may support the development of secure additive manufacturing environments for aerospace, space, defense, and other industries producing high-value or safety-critical components.