Methods and systems for aligning images of a specimen are provided. One method includes reducing noise in a test image generated for a specimen by an imaging subsystem thereby generating a denoised test image. The method also includes detecting one or more patterned features in the denoised test image extending in at least a horizontal or vertical direction. In addition, the method includes designating an area of the denoised test image in which the detected one or more patterned features are located as a region of interest in the denoised test image. The method further includes aligning the denoised test image to a reference image for the specimen using only the region of interest in the denoised test image and a corresponding area in the reference image.