We found that enhanced vapor condensation in nanopores and nanochannels on hydrophilic surfaces affects contrast and spatial resolution of the atomic force microscopy (AFM) imaging. It was demonstrated, that at ambient conditions the use of conventional Si probes may provide contrast inversion of the topography image of the hydrophilic samples with nano-sized surface features whereas use of the probes modified with hydrophilic Pt/C nanowires ensures adequate AFM imaging. The phenomenon of the AFM contrast inversion and the spatial resolution improvement effect obtained with the probes modified with the nanowires are discussed. The explanation of the phenomenon considering the shape of liquid meniscus in hydrophilic nanopores and nanochannels is proposed.