The current study delves into the physical characteristics, chemical composition, structure, and topography of composite fragments extracted from the surfaces of sub- and supersonic cruise missiles produced by the Russian Federation. This research analyzes the physical and chemical composition, structure, and surface topography of specialized structures crafted from composite materials. By employing scanning electron microscopy, our study provides valuable insights for establishing a scientifically grounded system for automatically identifying these specialized structures and discerning their country of origin based on international classifications. Fragments of Kh-101 and 9M727 “Iskander-K” cruise missiles were selected for research. The study utilized non-destructive testing methods to analyze the materials. Scanning electron microscopy enabled precise determination of the chemical composition, structure, and topology of composite structural members from Russian-produced cruise missiles. This precision promises to streamline the development of domestic missile defense systems by saving both time and resources.