A method for automatically controlling a system for separating biological fluids to remove air from a collection container into which a target product obtained by separation of the biological fluids has been flowed, the system comprising a disposable flow circuit including a tubing in fluid communication with the collection container and a durable hardware component including a pump (16, 18, 20) for engaging the tubing to flow fluid therethrough and a programmable controller for operating the pump, the method comprising: a) the programmable controller operating the pump in a first, forward direction to flow the target product into the collection container; b) the programmable controller determining that substantially all the target has been pumped into the collection container; and c) the programmable controller operating the pump in the first, forward direction to pump a chase volume of air into the collection container along with any target product remaining in the tubing, wherein after the chase volume of air is pumped into the collection container, a residual volume of air is contained in the collection container, wherein the residual volume of air comprises the chase volume plus an initial volume of air contained within the collection container after substantially all the target product has been pumped into the collection container but before pumping the chase volume of air into the collection container, wherein the initial volume of air is determined empirically, and a value for the initial volume of air in the collection container is pre-programmed into the controller; wherein the chase volume of air is calculated based on an internal diameter of the tubing and number of pump cycles required to pump the chase volume into the collection container; the method further comprising: d) the programmable controller calculating a value for the total volume of residual air; e) the programmable controller operating the pump in a second, reverse direction a sufficient number of cycles to remove the residual volume of air from the collection container; and f) the programmable controller stopping operation of the pump (16, 18, 20) when the amount of air removed from the collection container is substantially equal to the residual volume of air. a) the programmable controller operating the pump in a first, forward direction to flow the target product into the collection container; b) the programmable controller determining that substantially all the target has been pumped into the collection container; and c) the programmable controller operating the pump in the first, forward direction to pump a chase volume of air into the collection container along with any target product remaining in the tubing, wherein after the chase volume of air is pumped into the collection container, a residual volume of air is contained in the collection container, wherein the residual volume of air comprises the chase volume plus an initial volume of air contained within the collection container after substantially all the target product has been pumped into the collection container but before pumping the chase volume of air into the collection container, wherein the initial volume of air is determined empirically, and a value for the initial volume of air in the collection container is pre-programmed into the controller; wherein the chase volume of air is calculated based on an internal diameter of the tubing and number of pump cycles required to pump the chase volume into the collection container; d) the programmable controller calculating a value for the total volume of residual air; e) the programmable controller operating the pump in a second, reverse direction a sufficient number of cycles to remove the residual volume of air from the collection container; and f) the programmable controller stopping operation of the pump (16, 18, 20) when the amount of air removed from the collection container is substantially equal to the residual volume of air.