Methods for nanoimprint lithography using a deformable mold. Generally, the method includes a deformable mold fixed firmly onto a hollow mold holder around its full periphery is attached to top inner surface of the chamber and positioned underneath the transparent section. The central area of the mold is freely accessible from underneath through the opening of the mold holder. At beginning of the imprinting, the substrate with a layer of resist is positioned underneath the mold at a predetermined gap between them and a substrate is moved up to contact with the mold either under vacuum or under atmosphere. After consolidating the resist, the substrate is separated from the mold by either direct pull-down enabled by stage movement or deforming the mold enabled by differential pressure between the mold mini-chamber and the bulk volume of the chamber, or mixing of both.