To improve the reliability of the design of hard disk drives, this study aims to determine the effective elastic properties of disks with perfluoropolyether lubricant films on the diamond-like carbon overcoats of magnetic disks. However, the determination of the effective elastic modulus of multi-layered film from molecularly thin lubricant films (1.0 nm) and diamond-like carbon overcoats is extremely difficult because these layers are ultra-thin. Therefore, the method of etching in the depth direction with an Ar-gas cluster ion beam is proposed in this study. The lubricants D-4OH and Z-tetraol, comprising different main chains, are applied to the samples at varying thicknesses. Additionally, the D-4OH is UV-treated to vary the bonded film thickness. The effective Young's modulus of disk with D-4OH is approximately 60 and 20 GPa at 1.2 and 2.9 nm film thicknesses, respectively, whereas that of Z-tetraol is approximately 16 GPa at 1.2 nm film thickness, and exhibits less dependence on the film thickness than that of D-4OH. The effective Young's modulus of D-4OH increases with increasing bonded thickness. These results suggest a significant variation in the effective Young's modulus of disks with the lubricant film based on the film thickness, molecular structure, and adsorption state.