The controlled patterning of anisotropic gold nanoparticles is of crucial importance for many applications related to their optical properties. In this paper, we report that gold nanorods prepared by a seed-mediated synthesis protocol (without any further functionalization) can be selectively deposited on hydrophilic parts of hydrophobic–hydrophilic contrast patterned substrates. We have seen that, when nanorods with lengths much smaller than the width of the hydrophilic stripe are used, they disperse on these stripes with random orientation and tunable uniform particle separation. However, for nanorods having lengths comparable to the width of the hydrophilic stripes, confinement-induced alignment occurs. We observe that different interactions governing the assembly forces can be modulated by controlling the concentration of assembling nanorods and the width of the hydrophilic stripes, leading to markedly different degrees of alignment. Our strategy can be replicated for other anisotropic nanoparticles to produce well-controlled patterning of these nanoentities on surfaces.