Feature extraction is of great importance in condition monitoring and fault diagnosis of rolling machinery. Nonlinear Dimensionality Reduction (NDR) theories brought a new idea for recognizing and predicting the underlying nonlinear behavior. In this paper, we propose a NDR based feature extraction method for fault classification of rolling element bearing. Original feature spaces are constructed by time- and frequency-domain feature selection method, NDR-based feature exaction scheme is proposed to acquire the low-dimensional embeddings from feature space, which provide a more truthful low-dimensional representation compared to the linear DR methods. In order to systematically and quantitatively investigate the performance of NDR method, we compare the three nonlinear DR methods: Isometric Mapping(Isomap), Locally Linear Embedding (LLE),and Local Tangent Space Alignment(LTSA) with the intent of determining a reduced subspace representation in which the fault classes of rolling element bearing are more easily discriminable. Evaluation of the classification performance is done by Support Vector Machine (SVM), a supervised classifiers. Additionally, with optimal neighborhood size, binary code combinations based on NDR embedded results are given for fault recognition. Experiments on 6 fault data sets are used for fault and severity classification. Quantitative evaluation results suggest that NDR methods are superior in identifying potential novel classes within the data.