The goal of this paper is to bring forth a holonic organization for self-organization of holonic multi-agent systems with the support of stigmergy. An extension of the RIO model is confirmed by stigmergy to build self-organizing system that emphasizes the autonomy and cooperation of entities, thus more suited with a dynamic task environment. In this paper, a holonic stigmergy mechanism for tuning the emergence of organizational structures is introduced and it is illustrated that how it works on clustering process taking inspiration from the cemetery organization of ants.