A method of fabricating a target shallow trench isolation (STI) structure between devices in a wafer-level image sensor having a large number of pixels includes etching a trench, the trench having a greater depth and width than a target STI structure and epitaxially growing the substrate material in the trench for a length of time necessary to provide the target depth and width of the isolation structure. An STI structure formed in a semiconductor substrate includes a trench etched in the substrate having a depth and width greater than that of the STI structure, and semiconductor material epitaxially grown in the trench to provide a critical dimension and target depth of the STI structure. An image sensor includes a semiconductor substrate, a photodiode region, a pixel transistor region and an STI structure between the photodiode region and the pixel transistor region.