Polyether Ether Ketone (PEEK) is poised to revolutionize biomedical applications, leveraging its exceptional mechanical strength, chemical stability, and biocompatibility. To overcome its limitations, we pioneered a promising, data-driven methodology that integrates advanced data augmentation techniques with neural network modeling. This innovative approach systematically optimizes the surface modification of 3D-printed PEEK, focusing on pivotal metrics such as hydrophilicity, surface energy, cell viability, and antibacterial efficacy. This research offers a beacon of hope for the customization of PEEK-based implants and devices, empowering clinicians and patients alike with new possibilities for improved healthcare outcomes.