Utilization of the Marangoni effect in a liquid metal is investigated, focusing on initiating instabilities to direct material assembly via the Rayleigh Plateau instability. Thin (2 nm) copper (Cu) films are lithographically patterned onto thick (12 nm) nickel (Ni) Ships to induce a surface energy gradient at the maximum wavelength of the filament instability predicted by Rayleigh Plateau instability analysis. The pattern is irradiated with an 18 ns Pulsed laser such that, the pattern melts and the resultant Ni-Cu surface tension gradient induces Marangoni flows due to the difference in surface energies: The experiniental results, supported by extensive direct numerical simulations, demonstrate that the Marangoni flow exceeds, the capillary flow induced by the initial geometry, guiding instabilities such that final nanoparticle location is directed toward the regions of higher surface energy (Ni regions). Our work shows a route for manipulation, by means of the Marangoni effect, to direct the evolution of the surface instabilities and the resulting pattern formation.