A method of forming a silicon-on-insulator (SOI) semiconductor structure in a substrate having a bulk semiconductor layer, a buried oxide (BOX) layer and an SOI layer. During the formation of a trench in the structure, the BOX layer is undercut. The method includes forming a dielectric material on the upper wall of the trench adjacent to the undercutting of the BOX layer and then etching the dielectric material to form a spacer. The spacer fixes the BOX layer undercut and protects it during subsequent steps of forming a bottle-shaped portion of the trench, forming a buried plate in the deep trench; and then forming a trench capacitor. There is also a semiconductor structure, preferably an SOI eDRAM structure, having a spacer which fixes the undercutting in the BOX layer.