A multilayer approach (MA) and modified boundary conditions (MBC) are proposed as fast and efficient numerical methods for the design of 1D photonic structures with rough interfaces. These methods are applicable for the structures, composed of materials with an arbitrary permittivity tensor. MA and MBC are numerically validated on different types of interface roughness and permittivities of the constituent materials. The proposed methods can be combined with the 4x4 scattering matrix method as a field solver and an evolutionary strategy as an optimizer. The resulted optimization procedure is fast, accurate, numerically stable and can be used to design structures for various applications.