We present a low-cost overlay alignment metrology solution for nanoimprint lithographythat uses optical microscopy, displacement-sensing algorithms, and specially-designedimprint molds that include shallow alignment marks that are visible to the optical systembut do not pattern the wafer. This innovation reduces measurement distances to nearzero, the optimal distance for displacement-sensing algorithms, and allows foralignment marks to occupy the same piece of wafer real estate without interfering inany way, thus saving silicon area. Additionally, the method we present does notrequire the comparison of alignment marks between the wafer and the mold,thus removing process variations as a variable. We fabricate the shallow-markmolds, show that the shallow alignment marks indeed do not leave a mark onthe wafer, and, implementing our nDSE (nanoscale displacement sensing andestimation) techniques, we demonstrate nanoscale alignment to a precision of 35 nm,1−σ. Given sufficient engineering refinement, we would fully anticipate achieving alignmenterrors down to the 1 nm range using these methods.