A robust technique is presented for auto-aligning nanostructures to slow-etching planes during crystallographic etching of silicon. Lithographic mask patterns are modified from the intended dimensions of the nanostructures to compensate for uncertainty in crystal axis orientation. The technique was employed in fabricating silicon nanolines having lengths of 600 nm and widths less than 5 nm, subjected to intentional misalignment of up to . After anisotropic etching, the auto-aligned structures exhibited as little as 1 nm of width variation, as measured by a critical dimension atomic force microscope, across 2 deg of variation in orientation. By contrast, the widths of control structures fabricated without auto-alignment showed 8 nm of variation. Use of the auto-alignment technique can eliminate the need for fiducial-based alignment methods in a variety of applications.