A system for automated processing of a cell product comprising surface antigen expressing cells, in preparation for surface antigen expressing cell selection, the system comprising: a reusable separation apparatus controlled by a microprocessing controller unit driven by software, wherein the apparatus and microprocessing controller unit are configurable with a plurality of settings; a disposable sterile circuit configured to associate with the reusable separation apparatus, the disposable sterile circuit comprising a spinning membrane separator comprising a porous membrane, wherein the separator comprises an inlet and first and second outlets (46, 48); a cell product in communication with the inlet of the separator, wherein the separation apparatus is configured in a first cycle by the microprocessing controller to flow the cell product into the inlet of the separator, separate platelets and supernatant from the first outlet into a filtrate container, and separate remaining cellular components from the second outlet into an in-process container; wash media within a media container (135a, 135b) in communication with the in-process container, wherein the separator is configured by the separation apparatus in a second cycle to flow the wash media into the in-process container containing the remaining cellular components to form resuspended platelet-depleted cell product; an external injection port located on the in-process container configured to receive an agent having an association with the surface antigen expressing cells of the resuspended platelet-depleted cell product, wherein the in-process container is configured to incubate the agent with the surface antigen expressing cells over an incubation period sufficient for the agent to bind and/or associate with the surface antigen expressing cells to form a first mixture, comprising agent-target cell complexes, unbound/unassociated agent, and cells not presenting the antigen; wherein the separation apparatus is configured in a third cycle to separate the first mixture into unbound/unassociated agent, directed from the first outlet into the filtrate container, and a second mixture, comprising agent-target cell complexes and cells not expressing the antigen, directed from the second outlet to a retentate container, wherein the second mixture is ready for target cell selection. a reusable separation apparatus controlled by a microprocessing controller unit driven by software, wherein the apparatus and microprocessing controller unit are configurable with a plurality of settings; a disposable sterile circuit configured to associate with the reusable separation apparatus, the disposable sterile circuit comprising a spinning membrane separator comprising a porous membrane, wherein the separator comprises an inlet and first and second outlets (46, 48); a cell product in communication with the inlet of the separator, wherein the separation apparatus is configured in a first cycle by the microprocessing controller to flow the cell product into the inlet of the separator, separate platelets and supernatant from the first outlet into a filtrate container, and separate remaining cellular components from the second outlet into an in-process container; wash media within a media container (135a, 135b) in communication with the in-process container, wherein the separator is configured by the separation apparatus in a second cycle to flow the wash media into the in-process container containing the remaining cellular components to form resuspended platelet-depleted cell product; an external injection port located on the in-process container configured to receive an agent having an association with the surface antigen expressing cells of the resuspended platelet-depleted cell product, wherein the in-process container is configured to incubate the agent with the surface antigen expressing cells over an incubation period sufficient for the agent to bind and/or associate with the surface antigen expressing cells to form a first mixture, comprising agent-target cell complexes, unbound/unassociated agent, and cells not presenting the antigen; wherein the separation apparatus is configured in a third cycle to separate the first mixture into unbound/unassociated agent, directed from the first outlet into the filtrate container, and a second mixture, comprising agent-target cell complexes and cells not expressing the antigen, directed from the second outlet to a retentate container, wherein the second mixture is ready for target cell selection.