The near-surface mechanical properties of thin films as well as bulk materials are amongst the key parameters important for their application, and instrumented nanoindentation is a standard technique for determining these mechanical properties. However, it is known that the surface topography of the characterized materials may affect the nanoindentation data when a sharp indenter for small penetration depths (displacements) is used. A thin film of hydrogenated amorphous silicon carbide with a thickness of 1.0 μm was deposited on a silicon wafer by plasma-enhanced chemical vapour deposition. The cyclic nanoindentation was used to construct a depth profile of mechanical properties for the flat surface (0.5 nm roughness) of the thin film, which made it possible to determine its modulus of elasticity of 83 GPa and hardness of 8.6 GPa unaffected by the silicon substrate. Grains with a spherical cap geometry with a typical radius of 0.5 µm and a height of 60 nm are distributed along the flat surface of the film. The grains have the same mechanical properties as the deposited film. Depth profiles of mechanical properties were determined for different types of contact between the Berkovich indenter with a radius of 50 nm and the selected grain (grain top, grain foot, two or three grains); i.e. for these measurements the following applied - the radius of the tip curvature was less than grain radii (RBerkovich < Rgrain). Residual imprints after nanoindentation measurements were carefully observed by atomic force microscopy and scanning electron microscopy. The near-surface mechanical properties were significantly affected by the surface topography, and the determined modulus of elasticity and hardness were crucially under- or overestimated in the range of 50% to 100% compared to the real values. The nature of these deviations was discussed. The solution is to use cyclic nanoindentation performed on the flat surfaces or on the top of grains, followed by extrapolation of the depth profiles to the zero-contact depth (film surface).