In some embodiments, a gate structure with a spacer on its side may be used as a mask to form self-aligned trenches in a microelectronic memory, such as a flash memory. A first portion of the gate structure may be used to form the mask, together with sidewall spacers, in some embodiments. Then, after forming the shallow trench isolations, a second portion of the gate structure may be added to form a mushroom shaped gate structure.