The 1900 topographical model contains the embryo of Freud's subsequent theory development. As time went on, Freud altered his theories so as to promote understanding of the psychoanalytical process. In the course of these changes, some key terms became ambiguous and at times various theoretical levels were mixed together so that they became logically inadmissible. This has led to a muddled theoretical debate and a theory that is difficult to apply. The concept muddle is greatest at the level of the structural model. This article elucidates this, as well as how the muddle can be eliminated by starting from the affect theory of the topographical model based on the phenomenological and descriptive levels that concern experiences and actions, not neurophysiology. Freud was sure about the distinctive nature of his research. This paper tries to re-establish and clarify this insight, which at present has been lost.