In 1896, Sigmund Freud hesitated before calling his discovery “Psychoanalysis”. In the years 1896-1897, he uses the word metapsychology, which he takes up again in 1915 in order to situate his research beyond psychology. For Freud, psychoanalytic science refers to the clinic, to the description of clinical categories and symptom modalities. His analysis of the difficulties he met during treatments makes him elaborate new theoretical hypotheses. The chapter shows that psychoanalysis as science articulates its critical research to its unconscious topological structure; such a theoretical work implies a continuous development of its specific epistemology, its rationality and its realistic position in philosophy. Psychoanalysis develops under the pressure of questions coming from experience, which always refers to unconscious knowledge carried by each subject who is constituted by this very knowledge. Reformulating a thesis on the unconscious, taking into account its formal structure has its difficulties.