An oxide layer is formed over a substrate having a smaller isolation trench and a large isolation trench. A nitride layer is formed over the oxide layer such that it completely fills the smaller isolation trench and lines the larger isolation trench. The nitride layer is etched back to form a recess in the nitride layer in the smaller isolation trench while at least a portion of the nitride layer lining the larger isolation trench is completely removed. A layer of HDP oxide is deposited over the substrate, completely filling the smaller and larger isolation trenches. The HDP oxide layer is planarized to the upper surface of the substrate. The deeper larger isolation trench may be formed by performing an etching step after the nitride layer has been etched back, prior to depositing HDP oxide.