Precise 3D representation of complex materials, here the lithium-ion batteries, is a critical step toward designing optimized energy storage systems. One requires obtaining several such samples for a more accurate evaluation of uncertainty and variability, which in turn can be costly and time demanding. Using 3D models is crucial when it comes to evaluating the transport and heat capacity of batteries. Further, such models represent the microstructures more precisely where connectivity and heterogeneity can be detected. However, 3D images are hard to access, and the available images are often collected in two dimensions (2D). Such 2D images, on the other hand, are more accessible and often have higher resolution. In this paper, a deep learning method has been applied to take advantage of 2D images and build 3D models of heterogeneous materials through which more accurate characterization and physical evaluations can be achieved. While being trained using only 2D images, the proposed framework can be utilized to generate 3D images. The proposed method is applied to a few realistic 3D images of lithium-ion battery electrodes. The results indicate that the implemented method can reproduce important structural properties while the flow and heat properties are within an acceptable range.