The demand of ultra-precision micro-machine tools is growing day by day due to exigent requirements of miniaturized components. High accuracy, good dimensional precision and smooth surface finish are the major characteristics of these ultra-precision machine tools. High-speed machining has been adopted to increase the productivity using high-speed spindles. However, machine tool vibration is a major issue in high-speed machining. Vibration significantly deteriorates the quality of micro-machining in terms of dimensional precision and surface finish. This paper describes a design methodology of a closed type machine structure for vibration minimization of a high-speed micro-milling center. The rigid machine structure has provided plenty of stiffness and the damping capability to the machine tool without utilizing vibration absorbers . The models of the machine structures have been generated and assembled in AutoCAD 3D . The performances of the integrated micro-milling machine tools were determined by finite element analysis. The best model has been selected and proposed for manufacturing. Additionally, simulation results were validated by comparing with experimental results. Eventually, after manufacturing and assembly, experiments have been performed and determined that the amplitude of vibration was approaching towards nanometer level throughout the working range of the high-speed spindle. The machine tool was capable to fabricate miniaturized components with fine surface finish.