To enhance accuracy as well as efficiency in process of machining operations, the virtual machining systems are developed. Free from surfaces of sophisticated parts such as turbine blades, airfoils, impellers, and aircraft components are produced by using the 5-axis CNC machine tools which can be analyzed and developed by using virtual machining systems. The machining operations of thin walled structures such as impeller blades are with deflection errors due to cutting forces and cutting temperatures. The flexibility of thin walled impeller blades can cause machining defects such as overcut or undercut. So, the desired accuracy in the machined impeller blades can be achieved by decreasing the deflection error in the machining operations. To minimize the deflection of machined impeller blades, optimized machining parameters can be obtained. An application of virtual machining system in predicting and minimizing the deflection errors of 5-Axis CNC machining operations of impeller blades is presented in the study to increase accuracy and efficiency in process of part production. The finite element analysis is applied to obtain the deflection error in machined impeller blades. In order to minimize the deflection error of impeller blades in the machining operations, the optimization methodology based on the Genetic algorithm is applied. The impeller is machined by using the 5-axis CNC machine tool in order to validate the developed virtual machining system in the study. Then, the machined impeller is measured by using the CMM machines to obtain the deflection error. As a result, the deflection error of in machining operations of impeller by using 5-Axis CNC machine tools can be decreased in order to enhance accuracy and efficiency of part manufacturing.