Analysis of indentation data of heterogeneous material, in particular, layer on an elastic substrate requires information about the contact area that is essential for calculating mechanical properties. The actual shape of the AFM-tip is not described by simple body of revolution. In this work, the indentation of a stiff layer on a hyperelastic substrate by a truncated conical tip is studied using finite element methods. The size of the tip, elastic modulus, and thickness of the layer are varied. The obtained model dependences of loading and contact area versus the depth of indentation are used in analysis of the experimental data of AFM indentation of stiff inhomogeneous nanolayers of polyurethane surface. Thickness and elastic modulus of the layers, fracture properties of the surface are studied. The obtained results can find application in the study of mechanical properties and fracture toughness of thin flexible films on an elastic substrate.