Provided are a substrate processing method and a device manufactured by using the same, which may improve etch selectivity of an insulating layer deposited on a stepped structure. The substrate processing method includes: forming a first layer on a stepped structure having an upper surface, a lower surface, and a side surface connecting the upper surface and the lower surface; weakening at least a portion of the first layer; forming a second layer on the first layer; and performing an isotropic etching process on the first layer and the second layer.