Soft materials with an embedded stiffer layer are increasingly used in medical and sports engineering. A detailed understanding of the mechanical behavior of such a material system under localised load and resistance to indentation is very important. In this work, the deformation of an isotropic soft matrix with a buried stiffer thin layer under a circular flat indenter was investigated through finite element (FE) modeling. A practical approach in simulating the indentation resistance of such a system (soft matrix with a buried thin stiffer layer) is evaluated. The numerical result is correlated with the data based on analytical approaches for both homogeneous materials and elastic half space with an embedded stiffer layer. The influence of Poisson's ratio and auxeticity of the matrix on the deformation and indentation stiffness of the material system under different conditions (indenter size, sheet thickness, and embedment depth) were established and main influences of the Poisson's ratio on the material deformation and stresses are discussed. The result shows that the influence of matrix auxeticity on indentation resistance is highly depth dependent, with over 30% enhancement of the indentation resistance being predicted for materials with matrix of a negative Poisson's ratio.