This papers reports a three-dimensional (3D) extension of the model proposed by Groby et al. [J. Acoust. Soc. Am. 127, 2865-2874 (2010)]. The acoustic properties of a porous layer backed by a rigid plate with periodic rectangular irregularities are investigated. The Johnson-Champoux-Allard model is used to predict the complex bulk modulus and density of the equivalent fluid in the porous material. The method of variable separation is used together with the radiation conditions and Floquet theorem to derive the analytical expression for the acoustic reflection coefficient from the porous layer with 3D inhomogeneities. Finite element method is also used to validate the proposed analytical solution. The theoretical and numerical predictions agree well with the experimental data obtained from an impedance tube experiment. It is shown that the measured acoustic absorption coefficient spectrum exhibits a quasi-total absorption peak at the predicted frequency of the mode trapped in the porous layer. When more than one irregularity per spatial period is considered, additional absorption peaks are observed.