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Flat punch nanoindentation is a mechanical test used to obtain stress-strain relationships for thin soft layers on high stiffness substrates. To build upon the understanding of this nanoindentation test, Finite Element Analysis is conducted on varying geometries and material definitions using ABAQUS. The simulations created in ABAQUS provide an ideal environment and material. The data obtained through simulation is analysed in parallel with the experimental data obtained from nanoindentation to provide a comprehensive understanding of what is occurring on this nanoscale compression test. Through this process, it was concluded that the geometries of the thin films used in experimentation undergo a confinement effect due to the material of the film, which is expanding the area of the punch, confine the compressed material. Simulations for a uniaxial stress, uniaxial strain, and a large surface area thin film compression test (identical to experiment) were conducted. As predicted, the confinement that occurs during the uniaxial strain test, which is produced by halting all material from expanding while being compressed, is nearly identical to the confinement produced by the surrounding material during the large surface area thin film. Further simulations were performed on varying materials to develop a broader understanding of the physics occurring during experimentation. The material definitions consisted of Hyperfoams, crushable foams, and viscoelastic materials. The crushable foams demonstrated weak differences whether confined or not. This is due to the internal structural effect of having free volume causing the strain produced by compression to not cause the walls of the film to expand. Further experimentation is to be done on these materials to develop a comprehensive understanding of the physics occurring during the thin film compression of soft and biological materials.