PDMS (polydimethylsiloxane) is an important soft biocompatible material, which has various applications such as an implantable neural interface, a microfluidic chip, a wearable brain–computer interface, etc. However, the selective removal of the PDMS encapsulation layer is still a big challenge due to its chemical inertness and soft mechanical properties. Here, we use an excimer laser as a cold micro-machining tool for the precise removal of the PDMS encapsulation layer which can expose the electrode sites in an implantable neural interface. This study investigated and optimized the effect of excimer laser cutting parameters on the electrochemical impedance of a neural electrode by using orthogonal experiment design. Electrochemical impedance at the representative frequencies is discussed, which helps to construct the equivalent circuit model. Furthermore, the parameters of the equivalent circuit model are fitted, which reveals details about the electrochemical property of neural electrode using PDMS as an encapsulation layer. Our experimental findings suggest the promising application of excimer lasers in the micro-machining of implantable neural interface.