Out of distribution (OOD) detection remains a critical challenge in malware classification due to the substantial intra family variability introduced by polymorphic and metamorphic malware variants. Most existing deep learning based malware detectors rely on closed world assumptions and fail to adequately model this intra class variation, resulting in degraded performance when confronted with previously unseen malware families. This paper presents MADOOD, a novel two stage, cluster driven deep learning framework for robust OOD malware detection and classification. In the first stage, malware family embeddings are modeled using class conditional spherical decision boundaries derived from Gaussian Discriminant Analysis (GDA), enabling statistically grounded separation of indistribution and OOD samples without requiring OOD data during training. Z score based distance analysis across multiple class centroids is employed to reliably identify anomalous samples in the latent space. In the second stage, a deep neural network integrates cluster based predictions, refined embeddings, and supervised classifier outputs to enhance final classification accuracy. Extensive evaluations on benchmark malware datasets comprising 25 known families and multiple novel OOD variants demonstrate that MADOOD significantly outperforms state of the art OOD detection methods, achieving an AUC of up to 0.911 on unseen malware families. The proposed framework provides a scalable, interpretable, and statistically principled solution for real world malware detection and anomaly identification in evolving cybersecurity environments.