Polymethyl methacrylate (PMMA) is a material with good surface wettability and has unique and widespread applications in industrial fields. However, fabricating this material in an environmentally friendly way while maintaining its mechanical robustness remains a challenging task. One effective way is through the rational design of microstructure surfaces. The current study fabricated a pyramid microstructure array on a mold surface using offset-tool-servo flycutting, which was then combined with hot embossing to replicate an inverted pyramid microstructure array on a PMMA surface. Firstly, a toolpath compensation algorithm was developed to linearize the arc toolpath and reduce the cost of ultra-precision lathe. Then, the algorithm was further developed to achieve automatic linear toolpath intersection, aiming to ensure the machining accuracy and improve machining efficiency. An experiment testing the linear toolpath intersecting at 90° was conducted, fabricating a pyramid microstructure array with nanoscale roughness on the mold surface. This surface was then employed for replicating an inverted pyramid microstructure array on the PMMA surface using hot embossing. Furthermore, the accuracy of replication was evaluated, and the experimental results demonstrated excellent replication fidelity, exceeding 98%. The microstructural surface of the PMMA exhibited a change in surface wettability. The wettability test showed a water-droplet contact angle reduction from 84.8° ± 0.1° to 56.2° ± 0.1°, demonstrating a good hydrophilic effect. This study introduces a novel, environmentally friendly and high-precision method to fabricate a functional PMMA surface with an inverted pyramid microstructure array. The results of this study also provide strong technical support and theoretical guidance for micro-nanostructure functional surface machining and replicating.