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In a wide variety of InGaN/GaN quantum well (QW) structures, defects are observed which consist of a trench partially or fully enclosing a region of the QW having altered emission properties. For various different defect morphologies, cathodoluminescence studies suggest that the emission is redshifted in the enclosed region. Based on transmission electron microscopy and atomic force microscopy data, we suggest that the sub-surface structure of the trench defect consists of a basal plane stacking fault bounded by a stacking mismatch boundary, which terminates at the apex of a V-shaped trench.