Micro channels are widely used in microfluidics, and medical science for the extraction of DNA, electrophoresis, and blood protein analysis. In the current work, the wire electrical discharge machining (WEDM) process was used to fabricate micro channels on the stainless steel 316 (SS316) substrate. To check the feasibility of fabricating high-quality micro channels and thereafter micro-scale structures with the WEDM process the effect of different process parameters such as pulse-off time, pulse-on time, servo gap reference voltage and wire feed rate were investigated. The quality attributes taken were namely surface roughness of the channel base, overcut, micro channel depth, and material removal rate (MRR). The pulse-on time significantly affects surface roughness and MRR. The servo gap reference voltage is the key process parameter affecting the overcut and micro channel depth. It was observed from the parametric study that 15 µs pulse-on time, 35 µs pulse-off time, 17 v servo gap reference voltage, and 8 m/min wire feed rate are the optimum levels for getting high MRR, low surface roughness, less overcut and high micro channel depth. Additionally, the topographical, morphological, surface, and sub-surface characterization were also carried out to assess the surface integrity and extent of thermal damage caused by the WEDM process. With the optimum combination of process parameters a 6 × 6 micro needle array was successfully fabricated on the same substrate using micro channels as a basis of the fabrication process for the first time using the WEDM process.