Nuclear pore complexes (NPCs) mediate and control the transport of virtually all material between the cytosol and the nucleus. It is, therefore, unsurprising that they have long taken centre stage in physiology. A precise understanding of the NPC structure and function that remain to be thoroughly investigated yet is, thus, of crucial importance. The NPC can mediate transport both actively and passively. It remains to be clarified, however, whether transport of small molecules and macromolecules proceeds through the same route in the NPC. Furthermore, it has been shown that surface hydrophobicity represents a major sorting criterion for the active transport through NPCs. Transport factors like importin beta, which exhibit a rather large surface hydrophobicity, bind to their cargo and are believed to interact with a supposedly hydrophobic meshwork that is assumed to reside in the central channel of the NPC but has not yet been visualised. This interaction is presumed to lead to a partial breakdown of the meshwork, thereby, permitting the transport-cargo complexes to pass through. In this study, by using the nano-imaging approach, atomic force microscopy, we visualised under near-physiological conditions, for the first time, the presence of a hydrophobic meshwork in the NPC central channel. Furthermore, our data lend strong support for the existence of two segregated transport routes in the NPC.