In order to produce size-controllable Ag nanoparticles and a nanomesh-patterned Si substrate, we introduce a rapid thermal annealing(RTA) method and a metal assisted chemical etching(MCE) process. Ag nanoparticles were self-organized from a thin Ag film on a Si substrate through the RTA process. The mean diameter of the nanoparticles was modulated by changing the thickness of the Ag film. Furthermore, we controlled the surface energy of the Si substrate by changing the Ar or H2 ambient gas during the RTA process, and the modified surface energy was evaluated through water contact angle test. A smaller mean diameter of Ag nanoparticles was obtained under H2 gas at RTA, compared to that under Ar, from the same thickness of Ag thin film. This result was observed by SEM and summarized by statistical analysis. The mechanism of this result was determined by the surface energy change caused by the chemical reaction between the Si substrate and H2. The change of the surface energy affected on uniformity in the MCE process using Ag nanoparticles as catalyst. The nanoparticles formed under ambient Ar, having high surface energy, randomly moved in the lateral direction on the substrate even though the etching solution consisting of 10 % HF and 0.12 % H2O2 was cooled down to .20 oC to minimize thermal energy, which could act as the driving force of movement. On the other hand, the nanoparticles thermally treated under ambient H2 had low surface energy as the surface of the Si substrate reacted with H2. That’s why the Ag nanoparticles could keep their pattern and vertically etch the Si substrate during MCE.