Preparing a substrate with patterned regions for immersion based inspection

A system for preparing a substrate for immersion based inspection, wherein the substrate comprises three dimensional features, the system comprises a chamber;

• wherein the chamber comprises:
• an interface that is configured to receive an article comprising a substrate that comprises patterned regions, a housing, and a transparent element;
• wherein the transparent element is sealingly coupled to the housing to provide a sealed inner space;
• wherein sealed inner space comprises 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;
• one or more fluid pressure control units that are configured to:
• evacuate the gas from the gap while reducing a pressure within the chamber and maintaining an integrity of the transparent element;
• fill the gap with fluid while increasing the pressure within a chamber inner space and maintaining an integrity of the transparent element;
• and
• wherein the interface is configured to output the article from the chamber.