The directed assembly of arrayed nanoparticles is demonstrated by dictating the flow of a liquid phase filament on the nanosecond time scale. Results for the assembly of Ni nanoparticles on SiO2 are presented. Previously, we have implemented a sinusoidal perturbation on the edge of a solid phase Ni, thin film strip to tailor nanoparticle assembly. Here, a nonlinear square waveform is explored. This waveform made it possible to expand the range of nanoparticle spacing-radius combinations attainable, which is otherwise limited by the underlying Rayleigh-Plateau type of instability. Simulations of full Navier-Stokes equations based on volume of fluid method were implemented to gain further insight regarding the nature of instability mechanism leading to particle formation in experiments.