In the article it is shown that the nanopatterned interface of bimaterial is unstable due to the diffusion atom flux along the interface. The main goal of the research is to analyze the conditions of interface stability. The authors developed a model coupling thermodynamics and solid mechanics frameworks. In accordance with the Gurtin-Murdoch theory of surface/interface elasticity, the interphase between two materials is considered as a negligibly thin layer with the elastic properties differing from those of the bulk materials. The growth rate of interface roughness depends on the variation of the chemical potential at the curved interface, which is a function of interface and bulk stresses. The stress distribution along the interface is found from the solution of plane elasticity problem taking into account plane strain conditions. Following this, the linearized evolution equation is derived, which describes the amplitude change of interface perturbation with time.