The recent development of high-performance computing enables us to generate spatiotemporal high-resolution data of nonlinear dynamical systems and to analyze them for deeper understanding of their complex nature. This trend can be found in a wide range of science and engineering communities, which suggests that detailed investigations on efficient data handling in physical science must be required in future. To this end, we introduce the use of convolutional neural networks (CNNs) to achieve an efficient data storage and estimation of scientific big data derived from nonlinear dynamical systems.The CNN is utilized to reconstruct three-dimensional data from a few numbers of two-dimensional sections in a computationally friendly manner. The present model is a combination of two-and three-dimensional CNNs, which allows users to save only some of the two-dimensional sections to reconstruct the volumetric data. As an example of threedimensional data, we consider a fluid flow around a square cylinder at the diameter-based Reynolds number Re D of 300, and show that volumetric fluid flow data can successfully be reconstructed with the present method from as few as five sections. Furthermore, we also propose a combination of the present CNN-based reconstruction with an adaptive sampling-based super-resolution analysis to augment the data compression capability of the present methods. Our report can be a significant bridge toward practical data handling for not only the fluid mechanics field but also a vast range of physical sciences.