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Here, the use of top\u2010down inputs and controlled contextual cues is reported for the de novo fabrication of patterned dense collagen matrices with spatially varying tailored mesoscale structures. Initially, imposed electrical inputs are used to guide collagen triple helix molecules to partially assemble into a dense metastable molten fibril state that can be induced by permissive contextual cues (especially humidity) to undergo further assembly. Spatially\u2010controlled optical inputs that induce riboflavin\u2010based photo\u2010crosslinking can locally\u2010trap partially assembled states (e.g., molten fibrils). To illustrate the potential of collagen patterning, a functional corneal stromal substitute is specifically fabricated that mimics the microstructures of collagen in cornea\u2010sclera and demonstrates that it can restore histological structure and function in a corneal defect rabbit model. 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