We present NanoImprint lithography experiments and modeling of thin films of block copolymers (BCP). The NanoImprint technique is found to be an efficient tool not only to align lamellar phases perpendicularly to the substrate but also to get rid of in-plane defects over distances much larger than the natural lamellar periodicity. The modeling relies on self-consistent field calculations done in two- and three-dimensions and is found to be in good agreement with the experiments. It also offers some insight on the Nanolmprint lithography setup and on the conditions required to perfectly ordered BCP lamellae.