A method and apparatus for moving material in a multi-well plate includes applying positive and negative pressure to one or more wells in the plate, e.g., to enhance a flow rate of material from the well through a filter element. Wells requiring application of positive pressure may be identified, e.g., by image analysis performed by a machine vision system. Those wells determined to require enhanced throughput may have negative and positive pressure applied to the well, while other wells have only negative pressure applied.