Micro-fabrication is a technology that uses several methods in its application. There are 3 methods in micro-fabrication: physical process, chemical process, and biological process. The main methods used in material feeding are milling, chemical etching, and bio-machining. Each method will results surface roughness value. This research analyzes the surface roughness value by comparing each other to see the best surface roughness value in mold microfluidic application on copper. There are 2 methods to be compared, those are bio-machining and etching. Those methods are natural and random because the roughness produced doesn't have clear pattern. Research in etching method is done by variating time between 6, 8, 10 and 12 minutes. However, in bio-machining the time variations are 12 and 24 hours based on the previous research. Based on the research done, the optimum result for each method is obtained. For etching method, the best result obtained at 8 minutes with 2.03 μm surface roughness value & 31.89 μm depth. The best result for bio-machining obtained at 24 hours with 2.02 μm surface roughness value & 43.1 μm depth. Based on those values, it can be concluded that optimum value for etching has smaller depth compared to biomachining.