Atomic vapor cell is the most important component for atomic clock. A few vapor cells were fabricated based on multi-stack anodic bonding with four fabrication methods. By comparing with three traditional cavity fabrication methods and the first failed method by the laser drilling, it was found that the surface contamination induced in laser drilling and the roughness blocked the successful bonding. The surface roughness has to be less than 8 nm and in this case the method of laser drilling can be used successfully and with high efficiency, resulting in a novel process for atomic vapor cell fabrication with cavity.