Network monitoring systems that detect and analyze malicious activities as well as respond against them, are becoming increasingly important. As malwares, such as worms, viruses, and bots, can inflict significant damages on both infrastructure and end user, technologies for identifying such propagating malwares are in great demand. In the large-scale darknet monitoring operation, we can see that malwares have various kinds of scan patterns that involves choosing destination IP addresses. Since many of those oscillations seemed to have a natural periodicity, as if they were signal waveforms, we considered to apply a spectrum analysis methodology so as to extract a feature of malware. With a focus on such scan patterns, this paper proposes a novel concept of malware feature extraction and a distinct analysis method named “SPectrum Analysis for Distinction and Extraction of malware features(SPADE)”. Through several evaluations using real scan traffic, we show that SPADE has the significant advantage of recognizing the similarities and dissimilarities between the same and different types of malwares.