An apparatus for removing a defect according to the embodiment includes an image processing part for observing a surface of a substrate; a layer forming part for forming a layer on the surface of the substrate; and a humidity controlling part for controlling humidity in a chamber in which the substrate is placed. A method for removing a defect according to the embodiment includes detecting the defect on a surface of a substrate; forming an oxide layer by oxidizing the defect; and removing the oxide layer. A method for removing a defect according to another embodiment includes forming an oxide layer on an entire surface of a substrate; and removing the oxide layer to remove the defect.