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Au(001) surfaces that have been prepatterned into a rippled morphology develop one-dimensional nanodot arrays (nanobeads) selectively along the ripples when bombarded with energetic ions at an angle that is normal to the average surface orientation. By quantifying the shape and morphology of these arrays, we show experimentally and by numerical simulations of an extended Kuramoto-Sivashinsky equation that the degree of one-dimensional order of the nanobeads can be optimized by considering initial rippled surfaces with various wavelength and roughness values. Our simulations employ physical units and use the experimental topographies as initial conditions. Such nonideal shapes are key to elucidating the influence of nonlinear effects (like conformal interface motion and local redeposition) since the early stages of the dynamics for these prepatterned systems. In spite of the fact that the evolution of the surface morphology becomes far from trivial under these circumstances, our continuum model is able to reproduce the experimental results quantitatively, in contrast to relevant alternative models in the context of surface nanopatterning by ion-beam bombardment.