Material erosion of trench isolation structures in advanced semiconductor devices may be reduced by incorporating an appropriate mask layer stack in an early manufacturing stage. For example, a silicon nitride material may be incorporated as a buried etch stop layer prior to a sequence for patterning active regions and forming a strain-inducing semiconductor alloy therein, wherein, in particular, the corresponding cleaning process prior to the selective epitaxial growth process has been identified as a major source for causing deposition-related irregularities upon depositing the interlayer dielectric material.