The inherently high resolution of imprint lithography has the promise of extending integrated circuit minimum feature sizes down to the 10 nm region. However, the main effort of companies building nanoimprint tools has been directed to the development of robust printing techniques, rather than to alignment. Consequently, no alignment system currently exists for nanoimprint lithography that is capable of the alignment accuracy required by the semiconductor industry. This paper proposes a solution to the problem of obtaining accurate alignment over an extended imprinted area. On the one hand, alignment is difficult to perform when the mold template and the substrate are in contact, or nearly in contact. On the other hand, if they are widely separated, the accuracy is limited by the difficulty of simultaneously imaging fine features on both of them. However, by using orthogonal polarizations, sharp images of the template and substrate can be obtained when they are separated by 30 to 40 μm. Previous experience with a dual focus x-ray alignment microscope indicates that this alignment technique will readily meet the 18 nm 3 σ tolerance required by the semiconductor industry at the 45 nm node. Here the technique is adapted for nanoimprint lithography by employing transparent bulk mold materials (e.g. quartz) with opaque alignment targets on the surface. In addition, a flexure stage capable of reproducibly bringing the mold template and the substrate into contact is integrated into the system, so that after the alignment is performed it can be maintained during imprinting.