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Due to the shadowing effect, the oblique angle deposition technique can produce nanorods tilted toward the incident deposition flux. Periodic posts serving as seeds on a substrate allow the fabrication of nanorod arrays with controllable separations. However, in a conventional oblique angle deposition with no substrate rotation, nanorods grow faster along their widths in the direction perpendicular to the plane of incident flux. This anisotropic growth can result in 'fan-out' shapes of nanorods that touch each other due to the faster growing widths. Asymmetric two-phase substrate rotation was designed to eliminate the side growth in oblique angle deposition. In this method, the growing rods are exposed to the deposition flux from all angles with some portion of a rod surface receiving more flux than the rest. We fabricated well-aligned Si nanorod arrays with uniform sizes from templates arranged in square and triangular lattices using this two-phase substrate rotation method.