A method of processing a SOI substrate to form a groove in the SOI substrate in which a silicon layer is stacked on both sides of an oxide layer is disclosed. In accordance with an embodiment of the present invention, the method includes dividing a portion of the silicon layer, in which the groove is to be processed, into a plurality of unit portions, performing dry etching on certain portions of the plurality of divided unit portions such that the oxide layer is exposed and removing remaining portions of the plurality of divided unit portions by removing the oxide layer.