A method of forming self-aligned STI regions extending over portions of a Si substrate to enable the subsequent formation of epitaxially grown embedded S/D regions without using a lithography mask and the resulting device are provided. Embodiments include forming a STI etch mask with laterally separated openings over a Si substrate; forming shallow trenches into the Si substrate through the openings; forming first through fourth oxide spacers on opposite sidewalls of the shallow trenches and the openings; forming a deep STI trench between the first and second oxide spacers and between the third and fourth oxide spacers down into the Si substrate; forming a STI oxide layer over the first through fourth oxide spacers and a portion of the STI etch mask, the STI oxide layer filling the deep STI trenches; and planarizing the STI oxide layer down to the portion of the STI etch mask.