In sophisticated semiconductor devices, a semiconductor alloy, such as a threshold adjusting semiconductor material in the form of silicon/germanium, may be provided in an early manufacturing stage selectively in certain active regions, wherein a pronounced degree of recessing and material loss, in particular in isolation regions, may be avoided by providing a protective material layer selectively above the isolation regions. For example, in some illustrative embodiments, a silicon material may be selectively deposited on the isolation regions.