Quasi-aligned gold nanodots with a periodicity of ∼ 40 nm have been synthesized on a silica substrate by oblique deposition of gold on fast argon atom-beam-created nanoripples of wavelength 40 nm and subsequent annealing. The size distribution of these aligned nanodots resulting from oblique deposition at 85° of 0.5 nm Au film perpendicular to ripples is narrower than the similar deposition on a flat surface. The deposition and annealing process was simulated with a three-dimensional kinetic lattice Monte Carlo technique in order to understand the formation of aligned nanodots. The atomistic simulation and the experimental results suggest that there is an optimal thickness which can result in nanodots aligned along the ripples in the case of depositions perpendicular to the ripples. The nanodots formed after annealing of the films deposited parallel to ripples or on flat surface lack alignment.