1. A method of detecting defects, the method comprising: acquiring a first image of a detection region on a semiconductor substrate; acquiring a second image from the first image by performing a Fourier transform, which transforms a two-dimensional domain to a frequency domain, and performing a low pass filtering, which preserves a low frequency domain among the frequency domain and reduces a high frequency domain among the frequency domain; and detecting the defects in the detection region by comparing the second image with a reference image.