Malware detection on binary executables provides a high availability to even binaries which are not disassembled or decompiled. However, a binary-level approach could cause ambiguity problems. In this paper, we propose a new feature engineering technique that use minimal knowledge about the internal layout on a binary. The proposed feature avoids the ambiguity problems by integrating the information about the layout with structural entropy. The experimental results show that our feature improves accuracy and F1-score by 3.3% and 0.07, respectively, on a CNN based malware detector with realistic benign and malicious samples.