Laser focusing of neutral atoms into a periodic array of nanometre-scale features has emerged as a promising method of nanostructure fabrication. Laser cooled atoms interacting with a near-resonant laser standing-wave created above the substrate are focused into nodes or antinodes of the light intensity depending on the sign of the detuning of the laser frequency from the atomic resonance, thus forming periodic nanostructures. The physics beyond this deposition technique involves processes governing the interaction of light with atoms as well as the surface diffusion phenomena. We study the nanostructure growth using a laser standing-wave as a mask within a semiclassical trajectory tracing approach. The effect of surface diffusion is incorporated due to a real-time stochastic model. The results are compared with experimental data for chromium deposition.