We present the self-assembled formation of nanosized PFDTS (1H,1H,2H,2H-perfluorodecyltrichlorosilane) features on multilayered silica sphere arrays. We reveal the importance of residual water within the microsphere multilayers during PFDTS deposition and discuss a possible mechanism for the formation of the siloxane nanostructures. The multiscaled roughness induced by these superstructures is shown to lead to superhydrophobic behavior. The role of PFDTS is twofold: it (i) lowers the surface energy and (ii) provides the essential roughness to achieve superhydrophobicity. Moreover, the absence of PFDTS nanostructures on monolayers or in the absence of water leads to considerably smaller contact angles thereby indicating the relevance of multiscaled roughness for superhydrophobicity.