A semiconductor fabrication process includes patterning a hard mask over a semiconductor substrate to expose an isolation region and forming a trench in the isolation region. A flowable dielectric is deposited in the trench to partially fill the trench and a capping dielectric is deposited overlying the first oxide to fill the trench. The substrate may be a silicon on insulator (SOI) substrate including a buried oxide (BOX) layer and the trench may extend partially into the BOX layer. The flowable dielectric may be a spin deposited flowable oxide or a CVD BPSG oxide. The flowable dielectric isolation structure provides a buffer that prevents stress induced on one side of the isolation structure from creating stress on the other side of the structure. Thus, for example, compressive stress created by forming silicon germanium on silicon in PMOS regions does not create compressive stress in NMOS regions.