In the synthesis of nanostructures by pulsed laser deposition (PLD), a crucial role is played by the environmental deposition pressure and the substrate temperature. Due to the high temperature of nanoparticles (NPs) at landing, other factors may determine the structure of the resulting aggregates. Here, Au and TiO nanostructures are obtained by non-thermal fs-PLD in ambient conditions. On Si(100), only TiO NPs form fractals with areas up to ~ 1 × 10 nm, while on quartz Au NPs also form fractals with areas up to ~ 5 × 10 nm, a much smaller size with respect to the TiO case. The aggregation is described by a simple diffusive model, taking into account isotropic diffusion of the NPs, allowing quantitative simulations of the NPs and fractal area. The results highlight the key role of substrate thermal conductivity in determining the formation of fractals.