A new method for the accurate alignment of lithographically-defined patterns to the crystallographic axes of substrates is presented. We provide a lower (worst-case) limit of the achievable high aspect ratio using anisotropic wet chemical silicon etch for deep trenches. The method uses the fact that the intensity of light reflected from two sets of gratings, one on the photomask and the other on the substrate, is a sharp function of their relative angular misalignment. By using pre-etched gratings on the substrate formed by wet anisotropic etching, alignment accuracies better than 50 millidegrees with respect to silicon crystallographic axes have been demonstrated. Two types of microstructures—trenches with an aspect ratio >90:1 and silicon nanowires with widths <50 nm with atomically smooth etched facets—have been fabricated using i-line lithography to illustrate some applications of this alignment method. This all-optical method is readily applicable to industry-standard optical lithography and avoids the need for any individualized process steps, enabling cost-effective micro/nanostructure manufacturing.