We developed a new method to prepare aggregates of specific cells and immobilize cells on a substrate with specific shapes by using a synthetic multifunctional tool, which consisted of a cell adhesive Arg-Gly-Asp (RGD) sequence, a photoreactive phenyl azido group and a biotin group. This chemical nanotool, RGD-2-(6-[biotinamido]-2-(p-azidobenzamido)-hexaneamido)ethyl-1,3′-dithio-proprionate (RGD-BED) was added to human umbilical vein endothelial cells to bind to receptors via the ligand–receptor interaction. Next a photoimmobilization of the binding RGD-BED was carried out by UV irradiation to covalently couple a phenyl azido moiety of RGD-BED with the neighboring site of the integrin receptor. We found that not only the migration distance of RGD-BED immobilized cells was diminished, but also the cell morphology was fixed on the substrate due to the blocking of integrin receptors by RGD-BED. In contrast, the addition of biocytin-containing polymers, poly(N-methacryloyloxy biocytin-co-dimethylacrylamide), and avidin to the RGD-BED-immobilized cells led to restore cellular migration behavior, probably arising from the increase in the rigidity of the environment surrounding the cells. Furthermore, by the addition of avidin to the RGD-BED-immobilized cells, three-dimensional cell aggregates were formed due to the cross-linking of the biotin moieties of RGD-BED. These results show that RGD-BED is a potential nanotool not only to label and collect targeted cells by the formation of cell aggregates but also to suppress mobility and morphologies of specific cells to be applicable for medical treatments.