Recent research have depicted that hidden Markov model (HMM) is a persuasive option for malware detection. However, some advanced metamorphic malware are able to overcome the traditional methods based on HMMs. This proposed approach provides a two-layer technique to overcome these challenges. Malware contain various sequences of opcodes some of which are more important and help detect the malware and the rest cause interference. The important sequences of opcodes are extracted by eliminating partial sequences due to the fact that partial sequences of opcodes have more similarities to benign files. In this method, the sliding window technique is used to extract the sequences. In this paper, HMMs are trained using the important sequences of opcodes that will lead to better results. In comparison to previous methods, the results demonstrate that the proposed method is more accurate in metamorphic malware detection and shows higher speed at classification.