The structural and optical properties of trench defects, which are poorly understood yet commonly occurring defects observed on the surfaces of InGaN multiple quantum wells (MQW), are reported. These defects comprise near-circular trenches which enclose areas of MQW which give rise to a red shift in peak photoluminescence emission and a change in cathodoluminescence intensity with respect to the surrounding material. Atomic force microscopy shows that the height of trench-enclosed areas differs from that of the surrounding quantum well structure, and that trenches are unrelated to the commonly observed V-defects in InGaN films, despite being occasionally intersected by them. Cross-sectional electron microscopy analysis of trenches with raised centres suggests that the red shift in the observed cathodoluminescence peak emission may be due to the quantum wells being thicker in the trench-enclosed regions than in the surrounding quantum well area. The mechanism of trench formation and its implication for the control of the emission properties of light-emitting diodes is discussed.