An imprint lithography alignment method includes assessing a first alignment error between the template and the substrate, generating a first input signal corresponding to a first relative motion between the template and the substrate, initiating the first relative motion between the template and the substrate via the first input signal, assessing an output signal corresponding to the first relative motion, comparing the first input signal and the output signal to yield a motion control action corresponding to a second relative motion between the template and the substrate, generating a second input signal corresponding to the second relative motion between the template and the substrate, initiating the second relative motion between the template and the substrate via the second input signal, and assessing a second alignment error between the template and the substrate, wherein a magnitude of the first alignment error exceeds a magnitude of the second alignment error.