In this paper, the relevance of deep neural network (DNN) is studied in big data scenarios, specifically for prognostics applications. It is observed that fault predictions can be performed more efficiently when DNN is used with a pre-processing step. A novel hierarchical dimension reduction (HDR) approach is therefore proposed as a pre-processing step to DNN. This two-step approach is shown to be effective in extracting value from complex and uncertain big data. It is shown that use of HDR prior to DNN improves convergence and allows for the possibility of reduction in model size without any drop in accuracy. A comprehensive methodology is developed to facilitate prognostics using DNN. Simulation results are included to demonstrate the overall methodology using big data-sets.