Filling microstructures in the air with liquid or removing trapped gases from a surface in a liquid are required in processes such as cleaning, bonding, and painting. However, it is difficult to deform the gas–liquid interface to fill a small hole with liquid when surface tension has closed one end. Therefore, it is necessary to have an efficient method of removing gas from closed-end holes in liquids. Here, we demonstrate the gas-removing method using acoustic waves from small holes. We observed gas column oscillation by changing the hole size, wettability, and liquid surface tension to clarify the mechanism. First, we found that combining two different frequencies enabled complete gas removal in water within 2 s. From high-speed observation, about half of the removal was dominated by droplet or film formation caused by oscillating the gas column. The other half was dominated by approaching and coalescing the divided gas column. We conclude that the natural frequency of both the air column and the bubbles inside the tube are important.