Molecular level organization has been a subject of great relevance in supramolecular chemistry and nanotechnology. Supramolecular chemists count on the ability of molecules to form several kinds of organization, allowing the development of nanoscaled devices. In this way, the scanning probe microscopy provides a great tool for characterization, manipulation and interfacing such devices [1]. Regarding the ruthenium complexes [Ru(bpy)2Cl(BPEB)](PF6) and {[Ru(bpy)2Cl]2(BPEB)}(PF6)2, where bpy = 2,2'-bipyridine, the presence of the BPEB (1,4-bis[4-pyridyl)ethenyl]benzene) ligand has an important role as a recognition site for van der Waals interactions (Figure 1). On the other hand, cyclodextrins are macrocyclic molecules bearing a hydrophobic cavity that can support several types of guest molecules [2-3]. In this work we are showing the influence of the recognition site of the BPEB ligand and the formation of an inclusion compound in the patterning structures of films deposited over mica substrates, by SFM microscopy.