Abstract This work describes the process of fabrication of 3D topography membranes and the fully quantitative characterisation of their topography using atomic force microscopy (AFM), small-angle light scattering (SALS), scanning electron microscopy (SEM) and polarizing optical microscopy (POM). The use of these membranes and the impact of the 3D membrane topography on the enhancement of mass transport during solute recovery (hexyl acetate) from a viscous room temperature ionic liquid 1- n-butyl-3-methyl-imidazolium tetrafluoroborate ([C 4mim] [BF 4]) by organophilic pervaporation is presented and discussed. A quantitative analyses of the results obtained allow to conclude that the use of the surface-modified membrane led to an increase of solute flux of 14%, which is well above the value of 4% that may be attributed to an augment of membrane surface area due to the increased membrane roughness. This increase of solute flux has to be granted to improved fluid dynamic conditions due to micro-turbulence at the membrane surface. This work illustrates how the design of three-dimensional relief microstructures at the membrane surface, with topographic modulation of features with characteristic dimensions, may lead to improved momentum and mass transport conditions at the membrane surface through promotion of local micro-turbulence.