The Si surface after reactive ion etching (RIE) and different cleaning procedures was characterized by angle resolved X-ray photoelectron spectroscopy, high-resolution transmission microscopy, and atomic force microscopy. It was shown that CFx polymers, silicon carbides (Si-C bonds), and chemisorbed fluorine (Si-F), cover the silicon surface after RIE in a CHF3/C2F6 mixture. The last two residues penetrate the surface layer of a silicon substrate. CFx polymers are removed by oxygen plasma but Si-C and Si-F bonds related residues cannot be removed by "oxygen plasma/diluted HF" treatment. These compounds can be removed only by additional etching of the silicon surface layer. According to our experimental conditions a silicon consumption of 2.8 nm was enough to eliminate these compounds. By comparing different cleaning recipes and conditions it was found that O-2-plasma/HF/APM (ammonia-hydrogen peroxide mixture) provides the best cleaning characteristics. APM removes fluorine and carbon contamination by precise, controlled etching of silicon with high etch selectivity toward an SiO2 spacer. The silicon surface after the cleaning is quite smooth. It was demonstrated that the post spacer-etch cleaning of O-2-plasma/HF/APM is a robust process for Ti-salicide technology with respect to the reduction of the leakage current between poly-Si and source/drain.