Trench defects are a commonly occurring feature in InGaN/GaN quantum well (QW) structures. This defect appears at the surface of a structure as a trench enclosing a region of material with peculiar emission properties. Transmission electron microscopy was used to characterise the sub-surface structure of such defect. It consists of a basal-plane stacking fault (BSF) located in the QW stack and bound by a vertical stacking mismatch boundary (SMB) which runs towards the surface and which opens up into pits, which merge to form a trench. Atomic force microscopy and cathodoluminescence were performed on the same individual defects in order to directly correlate the morphology with the emission properties. A strong correlation has been established between the thickness of the trench and the redshift and intensity of the emission of the enclosed region suggesting that bright trench defects emitting at a longer wavelength nucleate early during the growth. Data also suggest that the SMB may act as a non-radiative recombination centre.