The specific mechanisms which leads to the formation of fractal nanostructures by pulsed laser deposition remain elusive despite intense research efforts, motivated mainly by the technological interest in obtaining tailored nanostructures with simple and scalable production methods. Here we focus on fractal nanostructures of titanium dioxide, $TiO_2$, a strategic material for many applications, obtained by femtosecond laser ablation at ambient conditions. We model the fractal formation through extensive Monte Carlo simulations based on a set of minimal assumptions: irreversible sticking and size independent diffusion. Our model is able to reproduce the fractal dimensions and the area distributions of the nanostructures obtained in the experiments for different densities of the ablated material. The comparison of theory and experiment show that such fractal aggregates are formed after landing of the ablated material on the substrate surface by a diffusive mechanism. Finally we discuss the role of the thermal conductivity of the substrate and the laser fluence on the properties of the fractal nanostructures. Our results represent an advancement towards controlling the production of fractal nanostructures by pulsed laser deposition.