Nanoindentation is an effective approach for measuring mechanical properties ofnanoscale films coated on substrates, yet results obtained through the classicOliver–Pharr model require additional consideration due to the existenceof a “substrate effect” when the film is much more compliant thanthe substrate. In this study, different models for removing this substrateeffect are compared, with focus on the Gao model, the Saha–Nix model, andthe Hay model and the use of a direct finite element (FE) approach is discussed.Validity of these models is examined using load–displacement dataobtained from simulated indentation of an elastic–plastic film in FEs. Itis found that the performance of the analytical models varies significantly withdifferent testing parameters, including ratio between film modulus and substratemodulus (Ef/Es),indenting ratio (hmax/film thickness), and yieldstrain. Choices of using a nanoindentation model to process experimental datashould be made according to estimated indentation depth and modulus differencebetween film and substrate. An example of applying substrate removal models toexperimental data is also shown.