Legal judgment prediction suffers from the problem of long case documents exceeding tens of thousands of words, in general, and having a non-uniform structure. Predicting judgments from such documents becomes a challenging task, more so on documents with no structural annotation. We explore the classification of these large legal documents and their lack of structural information with a deep-learning-based hierarchical framework which we call MESc; “Multi-stage Encoder-based Supervised with-clustering”; for judgment prediction. Specifically, we divide a document into parts to extract their embeddings from the last four layers of a custom fine-tuned Large Language Model, and try to approximate their structure through unsupervised clustering. Which we use in another set of transformer encoder layers to learn the inter-chunk representations. We analyze the adaptability of Large Language Models (LLMs) with multi-billion parameters (GPT-Neo, and GPT-J) with the hierarchical framework of MESc and compare them with their standalone performance on legal texts. We also study their intra-domain(legal) transfer learning capability and the impact of combining embeddings from their last layers in MESc. We test these methods and their effectiveness with extensive experiments and ablation studies on legal documents from India, the European Union, and the United States with the ILDC dataset and a subset of the LexGLUE dataset. Our approach achieves a minimum total performance gain of approximately 2 points over previous state-of-the-art methods.