An approach based on a lattice version of the Boltzmann kinetic equation for describing multiphase flows in nano- and microcorrugated devices is proposed. We specialize it to describe the wetting-dewetting transition of fluids in the presence of nanoscopic grooves etched on the boundaries. This approach permits us to retain the essential supramolecular details of fluid-solid interactions without surrendering--actually boosting--the computational efficiency of continuum methods. The method is used to analyze the importance of conspiring effects between hydrophobicity and roughness on the global mass flow rate of the microchannel. In particular we show that smart surfaces can be tailored to yield very different mass throughput by changing the bulk pressure. The mesoscopic method is also validated quantitatively against the molecular dynamics results of [Cottin-Bizonne, Nat. Mater. 2, 237 (2003)].