An imprint lithography system that pressurizes and depressurizes an air cavity behind a retained imprint template or substrate so as to deflect the template or substrate to aid in filling the template pattern with fluid resist and/or separating the template from the cured resist on the substrate. The system includes a controller, pressure sensors, and an impedance valve for modulating the air cavity pressure so as to reduce pressure wave oscillations within the cavity that otherwise negatively impact overlay accuracy control, fluid spread control and separation control.