The use of nanostructured materials in various technological applications such as microelectronics, sensors, membrane and filter technologies as well as medical applications (tissue engineering, drug delivery, implants,) is continuously increasing. There is an extensive research on controlling chemical (functional groups, surface charge, surface energy, wetting) and physical (porosity, surface topography) properties at nanoscale. Especially the control of wetting on nanoporous surfaces is of interest both from the fundamental and application point of view. Particularly the control of the wetting while keeping the unique characteristics such as high surface area and open pore structure is crucial for high performance membrane applications and technologies utilizing cell-surface interactions (advanced implants, cell isolation and separation, antifibrous surfaces). Here we demonstrated a novel approach to control the wetting of nanostructured surfaces without altering their topographic superior features. This approach is based on Initiated Chemical Vapour Deposition (iCVD) of fluorinated nano-polymer coatings. The capability of deposition at room temperature and with a high conformity makes iCVD an excellent tool to turn various types of surfaces into “Smart Surfaces” for instance in the field of medical applications.