The formation of silver cluster structures at submicrometer spatial scales under the irradiation by high-power femtosecond laser pulses with high repetition rate was observed in various glasses containing silver ions. In order to account for the formation of these structures in metal-doped glasses, we present a theoretical model for the organization of noble metallic clusters induced by a train of femtosecond laser pulses. The model includes photoionization and laser heating of the sample, diffusion, kinetic reactions, and dissociation of metallic species. This model was applied to reproduce the formation of cluster structures in silver-doped phosphate glass. The parameters of the silver structures were obtained numerically under various incident pulse intensities and number of pulses. Numerical modeling shows that the involved microscopic physical and chemical processes naturally lead to the emergence of a silver cluster organization, together with charge migration and subsequent trapping giving rise to a strong static electric field buried in the irradiated area as experimentally observed. Based on this modeling, a theoretical basis is provided for the design of new metallic cluster structures with nanoscale size.Read less <