Methods and structures for semiconductor devices with STI regions in SOI substrates is provided. A semiconductor structure comprises an SOI epitaxy island formed over a substrate. The structure further comprises an STI structure surrounding the SOI island. The STI structure comprises a second epitaxial layer on the substrate, and a second dielectric layer on the second epitaxial layer. A semiconductor fabrication method comprises forming a dielectric layer over a substrate and surrounding a device fabrication region in the substrate with an isolation trench extending through the dielectric layer. The method also includes filling the isolation trench with a first epitaxial layer and forming a second epitaxial layer over the device fabrication region and over the first epitaxial layer. Then a portion of the first epitaxial layer is replaced with an isolation dielectric, and then a device such as a transistor is formed second epitaxial layer within the device fabrication region.