The present disclosure provides a method of manufacturing a microelectronic device. The method includes forming recessed shallow trench isolation (STI) features in a semiconductor substrate, defining a semiconductor region between adjacent two of the recessed STI features; forming a tunnel dielectric feature within the semiconductor region; forming a nitride layer on the recessed STI features and the tunnel dielectric feature; etching the nitride layer to form nitride openings within the recessed STI features; partially removing the recessed STI features through the nitride openings, resulting in gaps between the nitride layer and the recessed STI features; and forming a first dielectric material on surfaces of the nitride layer, sealing the nitride openings.