A method for processing substrates includes providing a first substrate including a first region and a second region, the first region including a stack of a silicon oxide film and a silicon nitride film, the second region including a single layer of a silicon oxide film; etching the first substrate with a process gas including a sulfur containing gas, in accordance with varied flow rates of the sulfur containing gas, thereby determining each relationship between a given flow rate from among the varied flow rates of the sulfur containing gas and a shape difference between respective recessed portions formed in the first region and the second region; determining a flow rate of the sulfur containing gas on a basis of each relationship; and etching a second substrate at the determined flow rate of the sulfur containing gas.