Semiconductor devices and methods of forming thereof by post layer transfer fabrication of device isolation structures are described. A substrate with first and second major surfaces is provided. Circuit components may be formed on the first major surface of the substrate and a back-end-of-line (BEOL) dielectric layer is formed over the first major surface of the substrate which covers the circuit components. A single layer transfer is performed to expose the second major surface of the substrate for processing. The second major surface of the semiconductor substrate is processed to thin down the wafer, followed by a wafer thickness uniformity improvement process. One or more device isolation structures are formed through the semiconductor substrate from the second major surface of the semiconductor substrate.