Symmetric micro-supercapacitors with three dimensional (3D) interdigital electrode structures have been designed and fabricated through Carbon-microelectrochemical system (C-MEMS) technology. The micro-supercapacitor consists of a 3D C-MEMS structure which serves as a high effective surface area current collector and conformal polypyrrole (PPy) films deposited on the carbon structures as electroactive materials. The electrochemical performance of single electrodes and symmetric micro-supercapacitor cells were evaluated by cyclic voltammetry (CV) at different scan rates and galvanostatic charge/discharge tests. The effect of the 3D electrode structure on the performance of the micro-supercapacitor was studied. Single PPy/C-MEMS electrodes presented a specific capacitance of 162.07±12.40mFcm−2 and a specific power of 1.62±0.12mWcm−2 at 20mVs−1 scan rate. The symmetric micro-supercapacitor cells exhibited an average specific capacitance of 78.35±5.67mFcm−2 and a specific power of 0.63±0.04mWcm−2 at 20mVs−1 scan rate, demonstrating that 3D micro-supercapacitors are promising for applications that require high power in a limited footprint area of the device.