A cell processing system includes at least one processor connectable to a source container filled with a biological fluid, the at least one processor including a spinning membrane configured to receive and separate target cells from the biological fluid, the target cells exiting at a first outlet, one or more containers selectively connected to the first outlet； and, and a magnet. The system also includes a controller coupled to the at least one processor and configured to operate the spinning membrane to receive biological fluid from the source container and to direct the target cells to one of the one or more containers, to pause to permit magnetic particles to be associated with the target cells, and to operate the spinning membrane to receive the contents of one of the one or more containers with the magnet applied to the target cells associated with the magnetic particles..
