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The goal of Freud's Project was to place all psychological functioning on a neurological foundation; however, the resources of his time were inadequate for the task. This article attempts to link basic psychoanalytic and behavioral constructs to current neuroscience, specifically the memory paradigm of multiple trace theory. We propose that Freud's theory of early cognitive development, in which primary process is succeeded by secondary process, corresponds to the progression from a noncontextual taxon-based memory system to a locale system (mediated by hippocampal and cortical structures) in which memories are formed within space/time contexts. The effects of trauma within these models is then examined by noting how Freud's views of repression and regression parallel neuropsychological hypotheses about the ways in which traumatic experience impacts specific brain areas. Finally, the treatment implications of this theoretical synthesis are explored. We posit that transference resembles the learning theory construct of generalization, and the non-contextualized coding of the taxon system. In conclusion, we suggest that orthodox psychoanalytic approaches may have overestimated the efficacy of words and intellectual vectors in effecting therapeutic change. Nonverbal strategies may be required to reach material that is stored in early developing brain areas that may be inaccessible to words.