We study the mechanism of scarring of eigenstates in rectangular billiards with slightly corrugated surfaces and show that it is very different from that known in Sinai and Bunimovich billiards. We demonstrate that there are two sets of scar states. One set is related to the bouncing ball trajectories in the configuration space of the corresponding classical billiard. A second set of scar-like states emerges in the momentum space, which originated from the plane-wave states of the unperturbed flat billiard. In the case of billiards with one rough surface, the numerical data demonstrate the repulsion of eigenstates from this surface. When two horizontal rough surfaces are considered, the repulsion effect is either enhanced or canceled depending on whether the rough profiles are symmetric or antisymmetric. The effect of repulsion is quite strong and influences the structure of all eigenstates, indicating that the symmetric properties of the rough profiles are important for the problem of scattering of electromagnetic (or electron) waves through quasi-one-dimensional waveguides. Our approach is based on the reduction of the model of one particle in the billiard with corrugated surfaces to a model of two artificial particles in the billiard with flat surfaces, however, with an effective interaction between these particles. As a result, the analysis is conducted in terms of a two-particle basis, and the roughness of the billiard boundaries is absorbed by a quite complicated potential.