A method for separating one or more amino acids from a whole stillage byproduct produced in a corn dry milling process for making alcohol and system therefore is disclosed. In one embodiment, the method includes separating the whole stillage byproduct into an insoluble solids portion and a thin stillage portion, which include protein and amino acids. Thereafter, the thin stillage portion can be separated into a water soluble solids portion and a protein and amino acids portion. The resulting protein and amino acids portion can be separated into an amino acid(s) portion and a protein portion, both of which may be optionally dried, utilizing microfiltration, ultrafiltration, electrophoresis techniques/devices, or combinations thereof. The amino acid(s) in the resulting amino acid(s) portion may be further processed to be sold and/or used as or in, for example, nutritional supplements, flavor enhancers, animal feed additives, pharmaceuticals, industrial usage, fertilizers, herbicides, or as a feed source for other processing systems.