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