Machine learning has become a key tool in cybersecurity, improving both attack strategies and defense mechanisms. Deep learning models, particularly Convolutional Neural Networks (CNNs), have demonstrated high accuracy in detecting malware images generated from binary data. However, the decision-making process of these black-box models remains difficult to interpret. This study addresses this challenge by integrating quantitative analysis with explainability tools such as Occlusion Maps, HiResCAM, and SHAP to better understand CNN behavior in malware classification. We further demonstrate that obfuscation techniques can reduce model accuracy by up to 50%, and propose a mitigation strategy to enhance robustness. Additionally, we analyze heatmaps from multiple tests and outline a methodology for identification of artifacts, aiding researchers in conducting detailed manual investigations. This work contributes to improving the interpretability and resilience of deep learning-based intrusion detection systems