This research paper focuses on the fabrication of a microstructure based on a natural structure pattern of hydrophobic properties using micro-milling technology, followed by an investigation of the dimensional accuracy, roughness, and replication of the fabricated microstructure. Design, modeling (CAD system), fabrication, and replication are the steps of this process. Knowledge of biomimetics was used to select the microstructure. The main research aim of the experiments is to verify and extend the applicability of conventional CNC manufacturing technologies to obtain a functional surface structure. The micro-milling was carried out on a conventional DMG MORI CNC machine, a CMX 600 V three-axis horizontal milling center, using an external high-frequency electric spindle clamped to the machine. The machined material was aluminum alloy EN AW 7075. The tool was a 0.1 mm diameter double-edged ball mill made of sintered carbide and coated with TiSiN. The cutting conditions were determined according to the tool manufacturer’s recommendations. To compare the achieved accuracies, the same microstructure was fabricated using PLA technology. For subsequent replication of the sample, the negative of the selected microstructure was created and machined. Subsequently, a positive microstructure was created using the silicone impression material by the replication process. This paper and the experiments performed extend the technical knowledge in the field of manufacturing surface functional structures and confirm the possibility of manufacturing the designed structures using chip and laser machining technology, with achieved discontinuities in the range of 3 to 50 μm. They also highlight the issues of replication of such structures with respect to critical manufacturing locations (geometrical parameters of the structures affecting the functional properties of the structure, venting, replica defects, etc.).