In this work, we show how to control the morphology of femtosecond laser melted gold nanosphere aggregates. A careful choice of both laser fluence and wavelength makes it possible to selectively excite different aggregate substructures to produce larger spherical nanoparticles, nanorods, and nanoprisms or necklace-like 1D nanostructures in which the nanoparticles are interlinked by bridges. Finite integral technique calculations have been performed on the near-field concentration of light in the nanostructures which confirm the wavelength dependence of the light concentration and suggest that the resulting localized high intensities lead to nonthermal melting. We show that by tuning the wavelength of the melting light it is possible to choose the spatial extension of the ensembles of NPs heated thus allowing us to exhibit control over the morphology of the nanostructures formed by the melting process. By a proper combination of this method with self-assembly of chemically synthesized nanoparticles, one can envisage the development of an innovative high-throughput high-resolution nanofabrication technique.