An apparatus and method for processing a substrate using plasma, which has high plasma stability and process reproducibility, is provided. The method includes providing an apparatus for processing a substrate comprising a plasma generating region and a process region separate from the plasma generating region, placing the substrate including a silicon layer and an oxide layer in the process region, forming a hydrogen atmosphere in the process region by providing a hydrogen-based gas to the process region without passing through the plasma generating region, generating plasma by providing a fluorine-based gas to the plasma generating region, and providing the generated plasma to the process region to selectively remove the silicon layer compared to the oxide layer.