Master mold fabricated using micro milling is an easy way to develop the polydimethylsiloxane (PDMS) based microfluidic device. Achieving high-quality micro-milled surface is important for excellent bonding strength between PDMS and glass slide. The aim of our experiment is to study the optimal cutting parameters for micro milling an aluminum mold insert for the production of a fine resolution microstructure with the minimum surface roughness using conventional computer numerical control (CNC) machine systems; we also aim to measure the bonding strength of PDMS with different surface roughnesses. Response surface methodology was employed to optimize the cutting parameters in order to obtain high surface smoothness. The cutting parameters were demonstrated with the following combinations: 20,000 rpm spindle speed, 50 mm/min feed rate, depth of cut 5 μm with tool size 200 μm or less; this gives a fine resolution microstructure with the minimum surface roughness and strong bonding strength between PDMS-PDMS and PDMS-glass. © 2017 by the authors.