Data-driven models that act as surrogates for computationally costly 3D topology optimization techniques are very popular because they help alleviate multiple time-consuming 3D finite element analyses during optimization. In this study, one such 3D CNN-based surrogate model for the topology optimization of Schoen’s gyroid triply periodic minimal surface unit cell is investigated. Gyroid-like unit cells are designed using a voxel algorithm and homogenization-based topology optimization codes in MATLAB. A few such optimization data are used as input–output for supervised learning of the topology-optimization process via the 3D CNN model in Python code. These models could then be used to instantaneously predict the optimized unit cell geometry for any topology parameters. The high accuracy of the model was demonstrated by a low mean square error metric and a high Dice coefficient metric. The model has the major disadvantage of running numerous costly topology optimization runs but has the advantages that the trained model can be reused for different cases of TO and that the methodology of the accelerated design of 3D metamaterials can be extended for designing any complex, computationally costly problems of metamaterials with multi-objective properties or multiscale applications. The main purpose of this paper is to provide the complete associated MATLAB and PYTHON codes for optimizing the topology of any cellular structure and predicting new topologies using deep learning for educational purposes.