While the photopatterning of self-assembled monolayers (SAMs) has been extensively investigated, much less attention has been given to highly ordered multilayer systems. By being both thicker (0.5-2 μm) and more stable (cross-linked) than SAMs, patterned hybrid multilayers lend themselves more easily to the development of technology-relevant materials and characterization. This paper describes a facile two-step UV approach to patterning an alkylsilane multilayer by combining photoinduced self-assembly for multilayer synthesis and photodegradation through a mask for creating patterns within the film. In this second stage, a spatially resolved removal of the alkyl tail via a photooxidation mechanism took place, yielding regular and uniform silica microdomains. The result was a regular array of features (alkylsiloxane/silica) differing in chemical composition (hybrid/inorganic), ordering (crystal-like/disordered), and wettability (hydrophobic/hydrophilic). Such a photopatterned film was of utility for a range of applications in which water droplets, inorganic crystals, or aqueous polymer dispersions were selectively deposited in the hydrophilic silica microwells.