A method of processing a substrate includes providing a substrate including a pattern of lines extending in a first direction, and reducing stitching defects by removing material from the pattern of lines using a gas cluster beam. The pattern of lines includes a first subset of lines stitched to a second subset of lines in a stitching region that includes the stitching defects. The gas cluster beam includes an azimuthal component substantially parallel to the first direction. The stitching defects may be further reduced using an additional gas cluster beam in the opposite and substantially parallel to the first direction. The method may further include exposing a first region and a second region of a photosensitive layer of the substrate to different structured actinic radiation, and forming the pattern of lines on the substrate by developing the first region and the second region.