In this paper, optimal deep reactive ion etching (DRIE) process conditions for fused quartz were experimentally determined by Taguchi method, and fused quartz-based micro cantilevers were fabricated. In addition, comparative study on Q-factors of fused quartz and silicon micro cantilevers was performed. Using a silicon layer as an etch mask for fused quartz DRIE process, different 9 flow rate conditions of $C_4F_8$, $O_2$ and He gases were tested and the optimum combination of these factors was estimated. Micro cantilevers based on fused quartz were fabricated from this optimal DRIE condition. Through conventional silicon DRIE process, single-crystalline silicon micro cantilevers whose dimensions were similar to those of quartz cantilevers were also fabricated. Mechanical Q-factors were calculated to compare intrinsic damping properties of those two materials. Resonant frequencies and Q-factors were measured for the cantilevers having fixed widths and thicknesses and different lengths. The Q-factors were in a range of 64,000 - 108,000 for fused quartz cantilevers and 31,000 - 35,000 for silicon cantilevers. The experimental results supported that fused quartz had a good intrinsic damping property compared to that of single crystalline silicon.