Plasma treatment is a promising way of surface modification. In the case of heterogeneous materials, the study of the local properties of surfaces at the structural level is of interest. The changes of the surface of polyurethane (two-phase polymer, elastic modulus 25 MPa) under the action of argon plasma were studied by atomic force microscopy and finite-element modeling. The initial structure of polymer (stiff fibrils non-uniformly distributed in a softer matrix) is gradually destroyed during the treatment. The soft phase is etched and the roughness increases, especially in the areas of high concentration of the hard phase. A heterogeneous stiff carbon-containing nanolayer is formed on the surface; its thickness, elastic modulus, and adhesion depend on the local properties of the polymer and the duration of treatment. The materials have increased wettability and free surface energy, which made a positive effect on protein sorption.