We report on the elaboration of networks of SAM domains. More precisely, we show the feasibility in making arrays of functionalized alkylthiol nanodomains bordered with an alkylthiol matrix. The several step process relies on the replication of a self-organized cobalt array grown on Au(111). The SAM process takes place in solution. The chemical affinity of thiol for gold leads to the selective grafting of molecules on the surface. After having removed the inorganic array, alkylthiol functionalized with a terthiophene unit is grafted in free gold areas. The efficiency of the replication of the initial template depends on the stability of the first SAM. We also investigate electronic tunnel transport through oligothiophene islands with the STM. The variation of the molecular contrast with bias voltage between the two molecular species indicates a potential resonant tunneling mechanism through the orbitals of the aromatic compound.