Recently micro cutting has been applied to manufacturing of micro devices. Burr formation is a troublesome problem in micro cutting. From the point of view of the required accuracy, burr removal in the micro manufacturing cannot be performed by the manual operations or the additional cuttings. The paper presents a deburring process to remove the burrs on the micro-scale structured surfaces, which are machined in micro milling. In order to remove the burrs on the pillars in the structures, the study examines burr removal milling, polishing and water jet finishing. Burr removal milling leaves the cutter traces with adhesion of the chips on the pillars. Polishing finishes the surfaces with removing the burrs on the top of the pillars. A supporting device is used for protecting the edge shapes of the pillars in polishing. Then, the burrs on the side of the pillars can be removed in water jet finishing. A water jet machine driven by a low pressure pump is developed to remove the burrs without losing their shapes. The process sequence of polishing and water jet finishing is effective in removing the burrs in micro milling. The presented process is discussed to manufacture the micro-scale structures in mechanical manner based on the axiomatic design.