A method of forming a semiconductor device includes depositing a fill material (4) on a substrate portion (2) and on a dielectric layer (3) being disposed on the substrate (1) and having an opening (10) located above the substrate portion (2), removing the fill material (4) disposed above the dielectric layer (3), thereby leaving an exposed top surface (6) of the dielectric layer (3) and residual fill material (15) within the opening (10), forming a hard mask material (5) on the exposed top surface (6) of the dielectric layer (3) and on the residual fill material (15), patterning the hard mask material (5) for forming a hard mask (25) having trenches (8a, 8b) extending along a lateral direction (X) and exposing portions of the residual fill material (15) adjacent to the dielectric layer (3) and portions of the dielectric layer (3) adjacent to the residual fill material (15), anisotropically etching the dielectric layer (3), the residual fill material (15) and the substrate (1) selectively to the hard mask (5), thereby forming at least a first and a second isolation trench (11a, 11b) extending along the lateral direction (X).