Controlling the alignment and orientation of nanorods on various surfaces poses major challenges. In this work, we investigate hydrodynamic confinement and capillary alignment of gold nanorod assembly on chemically stripe-patterned substrates. The surface patterns consist of alternating hydrophilic and hydrophobic micrometer wide stripes; a macroscopic wettability gradient enables controlling the dynamics of deposited suspension droplets. We show that drying of residual liquid on the hydrophilic stripes gives rise to spatially localized deposition and alignment of the nanorods. Moreover, a universal relation between the extent of order within the single layers of nanoparticles and the lateral dimension of the deposits is presented and discussed.