Malware threats pose new challenges to analytic and reverse engineering tasks. It is needed for a systematic approach to that analysis, in an attempt to fully uncover their underlying attack vectors and techniques and find commonalities between them. In this paper, a method of malware analysis is described, together with a report of its application to the case of Flame and Red October. The method has also been used bv different analysts to analyze other malware threats like 'Stuxnet', 'Dark Comet', Toison Ivy', 'Locky', 'Careto', and 'Sofacy Carberp'. The method presented in this work is a systematic and methodological process of analysis, whose main objective is the acquisition of knowledge as well as to gain a full understanding of a particular malware. Using the proposed method to analyze two well-known malware as 'Flame' and 'Red October' will help to understand the added value of the method.