Abstract: Spectacular progress in developing advanced Si circuits with reduced size, along the track of Moore's law, has been relying on necessary developments in wet cleaning of nanopatterned Si wafers to provide contaminant free surfaces. The most efficient cleaning is achieved when complete wetting can be realized. In this work, ordered arrays of silicon nanopillars on a hitherto unexplored small scale have been used to study the wetting behavior on nanomodulated surfaces in a substantial range of surface treatments and geometrical parameters. With the use of optical reflectance measurements, the nanoscale water imbibition depths have been measured and the transition to the superhydrophobic Cassie-Baxter state has been accurately determined. For pillars of high aspect ratio (about 15), the transition occurs even when the surface is grafted with a hydrophilic functional group. We have found a striking consistent deviation between the contact angle measurements and the straightforward application of the classical wetting models. Molecular dynamics simulations show that these deviations can be attributed to the long overlooked atomic-scale surface perturbations that are introduced during the nanofabrication process. When the transition condition is approached, transient states of partial imbibition that characterize intermediate states between the Wenzel and Cassie-Baxter states are revealed in our experiments.