While linear systems have been useful in solving problems across different fields, the need for improved performance and efficiency has prompted them to operate in nonlinear modes. As a result, nonlinear models are now essential for the design and control of these systems. However, identifying a nonlinear system is more complicated than identifying a linear one. Therefore, modeling and identifying nonlinear systems are crucial for the design, manufacturing, and testing of complex systems. This study presents using advanced nonlinear methods based on deep learning for system identification. Two deep neural network models, LSTM autoencoder and Normalizing Flows, are explored for their potential to extract temporal features from time series data and relate them to system parameters, respectively. The presented framework offers a nonlinear approach to system identification, enabling it to handle complex systems. As case studies, we consider Duffing and Lorenz systems, as well as fluid flows such as flows over a cylinder and the 2-D lid-driven cavity problem. The results indicate that the presented framework is capable of capturing features and effectively relating them to system parameters, satisfying the identification requirements of nonlinear systems.