Provided are methods and systems for imprinting a pattern formed on surfaces of an imprint mask onto a double-sided substrate. The method includes deforming the surfaces of the first and second imprint stamps to produce respective first and second deformed surfaces, each having an arc therein. A pressure is applied to bring the deformed first and second surfaces into intimate contact with the first and second substrate surfaces, respectively. The applied pressure substantially flattens the deformed surfaces. To separate the two surfaces, the applied pressure is released. The method also includes transporting a substrate having first and second patterning surfaces and a shaped edge using a carrier having a holding portion that holds the shaped edge of the substrate, the holding surface having a shape that is complementary to the shaped edge of the substrate, such that the patterning surfaces remain untouched by the carrier.