The paper deals with the generalization of the scheme for asymptotic integration of waveguide equations for the case of a three-dimensional irregular waveguide layer. The boundary-value problem for the Helmholtz equation is considered. The case, when the space scale of a local wall heterogeneity is not too great, and the diffraction effects should be taken into account in proper wave description, is discussed. The general results are illustrated taking as an example a heterogeneity with the Gaussian law of the wall height change.