Methods 300 and 350 are disclosed for fabricating shallow isolation trenches and structures in multi-bit SONOS flash memory devices. One method aspect 300 comprises forming 310 a multi-layer dielectric-charge trapping-dielectric stack 420 over a substrate 408 of the wafer 402, for example, an ONO stack 420, removing 312 the multi-layer dielectric-charge trapping-dielectric stack 420 in a periphery region 406 of the wafer 402, thereby defining a multi-layer dielectric-charge trapping-dielectric stack 420 in a core region 404 of the wafer 402. The method 300 further comprises forming 314 a gate dielectric layer 426 over the periphery region 406 of the substrate 408, forming 316 a first polysilicon layer 428 over the multi-layer dielectric-charge trapping-dielectric stack 420 in the core region 402 and the gate dielectric 426 in the periphery region 406 , then concurrently forming 318 an isolation trench 438 in the substrate 408 in the core region 404 and in the periphery region 406. Thereafter, the isolation trenches are filled 326 with a dielectric material 446, and a second polysilicon layer 452 that is formed 332 over the first polysilicon layer 428 and the filled trenches 438, forming an self-aligned STI structure 446. The method 300 avoids ONO residual stringers at STI edges in the periphery region, reduces active region losses, reduces thinning of the periphery gate oxide and the ONO at the STI edge, and reduces dopant diffusion during isolation implantations due to reduced thermal process steps.
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