Regular arrays of Si nanorods with a circular cross section in hexagonal-closed-packed and triangular cross section in honeycomblike arrangements were grown using glancing angle deposition on Si100 and fused silica substrates that were patterned with Au dots using self-assembled mono- and double layers of polystyrene nanospheres as an evaporation mask. The Au dots were used as an etching mask for the underlying silica substrates in a reactive ion beam etching process, which greatly enhanced the height of the seeding spaces for the subsequent glancing angle deposition. An elongated shadowing length l of the prepatterned nucleation sites and less growth of Si structures between the surface mounds could be achieved this way. Differences in form, height, and diameter of the Si nanorods grown on either hcp or honeycomb arrays are explained by purely geometrical arguments. Different seed heights and interseed distances are found to be the main reasons for the strong distinctions between the grown nanorod arrays.