We study a novel ensemble approach for feature selection based on hierarchical stacking in cases of non-stationarity and limited number of samples with large number of features. Our approach exploits the co-dependency between features using a hierarchical structure. Initially, a machine learning model is trained using a subset of features, and then the model's output is updated using another algorithm with the remaining features to minimize the target loss. This hierarchical structure allows for flexible depth and feature selection. By exploiting feature co-dependency hierarchically, our proposed approach overcomes the limitations of traditional feature selection methods and feature importance scores. The effectiveness of the approach is demonstrated on synthetic and real-life datasets, indicating improved performance with scalability and stability compared to the traditional methods and state-of-the-art approaches.