The technologies used by the malicious codes have been being advanced and complicated through a merge of the existing techniques, while the damages by the malicious codes are moving from individuals and industries to organizations and countries. In this situation, the security experts are corresponding with the static analysis and the dynamic analysis such as signature searching and reverse engineering, respectively. However, they have had a hard time to respond against the obfuscated intelligent new zero day malicious codes. Therefore, it is required to prepare a process for a preliminary investigation and consequent detailed investigation on the infection sequence and the hiding mechanism to neutralize the malicious code. In this paper, we studied the formalization of the process against the infection sequence and the file hiding techniques with an empirical application to the Rustock malicious code that is most notorious as a spammer. Using the result, it is expected to promptly respond to newly released malicious codes.