This paper describes a hybrid process of Micro EDM and ECM to fabricate 3D microstructures. Micro electro discharge servo scanning machining (Micro EDSSM) is used to remove most part of workpiece material with fast machining speed, while Micro electrochemical scanning machining (Micro ECSM) with side-insulated tool electrode is used to remove the residual material and form the final 3D-structure surface. The application of side-insulated electrode during Micro ECSM is a key technological method to improve the machining accuracy of hybrid process. The effect of side-insulation film property to the movement of hydrogen bubble generated during Micro ECSM is discussed. The hydrophobic film can reduce damages to the junction between film edge and tool-electrode through the attraction to hydrogen, and a hydrophilic 704-silica material is firstly introduced for the fabrication of side-insulation film on the micro rod tool electrode by spin-coating technique. The 704-silica insulation film can effectively isolate the side of tool electrode with electrolyte. Micro 3D structures with uniform side-machining gap and small tape side-wall are machined. The surface with no heat-influence layer and 0.52μm Ra has been achieved.