A novel alignment system for imprint lithography in the deep sub-hundred nanometer realm is proposed. The new system is inherently more precise than the alignment systems used in conventional projection lithography because alignment marks on an imprint mold (the functional equivalent of a photomask in projection lithography) are directly compared to alignment marks on a wafer with no intermediate optics or reference points. If the measured misalignment is so severe that all marks cannot be brought into registration simultaneously by the usual x-y translations and rotations, the mold is deliberately deformed with a system of piezoelectric actuators in such a way that its induced distortions precisely match those on the wafer and all of the alignment marks at each chip site can be pulled into registration simultaneously. Finite-element analysis indicates that using actuators to distort the mold is superior to distorting the wafer.