A method and a system for preparing a substrate with three dimensional features for immersion based inspection. The method may include (a) receiving, by a secondary chamber, an article that includes the substrate, a housing, and a transparent element; wherein the transparent element is sealingly coupled to the housing to provide a sealed inner space; wherein the sealed inner space may include a gap between a first surface of the substrate to a second surface of the transparent element; wherein the gap is filled with gas during the receiving of the article; (b) evacuating the gas from the gap while reducing a pressure within the secondary chamber and maintaining an integrity of the transparent element; (c) filling the gap with fluid while increasing the pressure within a secondary chamber inner space and maintaining an integrity of the transparent element; and (d) outputting the article from the secondary chamber.