In aspects of the present invention, a method of forming a semiconductor device is disclosed, wherein amorphous regions are formed at an early stage during fabrication and the amorphous regions are conserved during subsequent processing sequences, and an intermediate semiconductor device structure with amorphous regions are provided at an early stage during fabrication. Herein a gate structure is provided over a semiconductor substrate and amorphous regions are formed adjacent the gate structure. Source/drain extension regions or source/drain regions are formed in the amorphous regions. In some illustrative embodiments, fluorine may be implanted into the amorphous regions. After the source/drain extension regions and/or the source/drain regions are formed, a rapid thermal anneal process is performed.