An apparatus for processing a substrate is provided. The apparatus includes a chamber having at least one gas inlet and at least one gas outlet, a substrate support in the chamber, a plasma generator and a controller configured to cause (a) placing a substrate on the substrate support, the substrate including a target layer having a recess, (b) exposing the substrate to a silicon-containing precursor, thereby forming an adsorption layer on a sidewall of the recess, (c) generating a plasma from a gas mixture in the chamber, the gas mixture including an oxygen-containing gas and a halogen-containing gas, (d) exposing the substrate to the plasma, thereby forming a protection layer on the adsorption layer while etching a bottom of the recess and (e) repeating (b) to (d) in sequence.