This paper aims at designing a 3-axis micro-milling machine to achieve high machining volumetric accuracy. The paper describes the optimization analysis of a micro-milling machine in its initial design phase. An initial design concept is selected according to criteria among various design concepts considered. Robust design method is applied using optimization analysis after comparing different Design of Experiments techniques. The mathematical model encompasses machine design variables and the inherent geometric errors. The volumetric error is considered as the objective function in the optimization analysis. Commercial optimization software is employed to apply different DOE techniques defined for this case with the Optimization Algorithms. The resulted designs are then filtered at the optimized design space and are further used to find the tolerance bands of each error variable in the model.