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We report on the fabrication of high-quality opaline photonic crystals from large silica spheres (diameter of 890 nm), self-assembled in hydrophilic trenches of silicon wafers by using a novel technique coined a combination of “lifting and stirring”. The achievements reported here comprise a spatial selectivity of opal crystallization without special treatment of the wafer surface, a filling of the trenches up to the top, leading to a spatially uniform film thickness, particularly an absence of cracks within the size of the trenches, and finally a good 3D order of the opal lattice even in trenches with a complex confined geometry, verified using optical measurements. The opal lattice was found to match the pattern precisely in width as well as depth, providing an important step toward applications of opals in integrated optics.