This paper proposes a methodology method for line edge roughness (LER) measurement and characterization using atomic force microscope. The definition and origins of LER are discussed firstly. A LER quantificational method using image processing and threshold method is presented, which is used to analyze AFM images of Silicon lines and extract LER characteristics. Then the energy distribution of LER is determined by the multi-scale analysis based on wavelet transform and the parameters of multi-scale characterization were given. The experiment data shows that this method can offer an effective quantitative analysis of LER.