The present invention is directed towards a method for patterning first and second substrates in a nanoimprint lithography system, the method including, inter alia, positioning the first substrate on a first substrate chuck; positioning a nanoimprint material on the first substrate; obtaining a spatial relationship between the first substrate and a nanoimprint mold assembly and imprinting a pattern in the nanoimprint material on the first substrate with the nanoimprint mold assembly while concurrently positioning the second substrate on a second substrate chuck; separating the nanoimprint mold assembly from the nanoimprint material on the first substrate; positioning a nanoimprint material on the second substrate; removing the first substrate from the first substrate chuck while concurrently obtaining a spatial relationship between the second substrate and the nanoimprint mold assembly and imprinting a pattern in the nanoimprint material on the second substrate with the nanoimprint mold assembly; and separating the nanoimprint mold assembly from the nanoimprint material on the second substrate, with the first and second substrates being subjected to substantially the same process conditions.