Hot embossing master is indispensable for the fabrication of polymeric optical waveguides using hot embossing technology. Sidewall roughness of silicon master is directly related to optical loss of optical waveguides In this paper, a silicon master was fabricated by using a deep-RIE process. Additionally, thermal oxidation followed by oxide removal was carried out to minimize etched Si sidewall roughness. Thermal oxidation and oxide removal were performed with $H_2O_2$ atmosphere at $1050^{circ}C$ and $NH_4$F:HF=6:l BOE, respectively, for the oxide thickness of 400$AA$, 1000$AA$, 3000$AA$, 4500$AA$, 5600$AA$ and 6200$AA$. The sidewall roughness was characterized by SEM and SPM-AFH measurements. We found that the roughness was improved from 12nm (RMS) to 6nm (RMS) for the scalloped sidewall and from 162nm (RMS) to 39nm (RMS) for the vertical striation sidewall, respectively.