This study combines atomic force microscope (AFM) nanoindentation tests and peridynamic (PD) simulations to extract the elastic moduli of polystyrene (PS) films with varying thicknesses. AFM nanoindentation tests are applied to relatively hard PS thin films deposited on soft polymer (polydimethylsiloxane (PDMS)) substrates. Linear force versus deformation response was observed in nanoindentation experiments and numerical simulations since the soft PDMS substrate under the stiff PS films allowed bending of thin PS films instead of penetration of AFM tip towards the PS films. The elastic moduli of PS thin films are found to be increasing with increasing film thickness. The validity of both the simulation and experimental results is established by comparison against those previously published in the literature.