The concept of the self is often treated either as a metaphysical primitive or as a uniquely human phenomenon inseparable from consciousness. Both approaches generate deep and persistent confusion. In this paper, I offer a clarification not a new metaphysical theory of the concept of self by grounding it firmly in physical reality and in actual scientific practice. The central claim is simple but easily misunderstood: the self is always a physical system composed of physical constituents, while our understanding of that system is mediated through abstract models. To make this precise, the paper distinguishes between empirical selves, which are physically instantiated systems that exist independently of our descriptions, and axiomatic selves, which are model-level representations constructed in abstract space. Experiential selfhood, including the human sense of "I," is treated as a particular axiomatic self instantiated in neural structure one model among many for the same empirical system. No additional ontological category of self is introduced. The framework is illustrated through detailed parallel with a physical case study of light, where a single empirical phenomenon (light) admits multiple non-equivalent models (ray, wave, particle, quantum field). Just as wave and particle models are both valid representations of light without ontological conflict, biological and experiential models are both valid representations of the human organism. A major refinement concerns the notion of a physical system itself: systems are not intrinsically well-defined in nature but are selected as objects of study, becoming well-defined relative to the success of modeling. By making these distinctions explicit and illustrating them through systematic comparison, this framework dissolves long-standing confusions about identity, persistence, consciousness, anthropocentrism, and the mind-body problem.