At this study, after designing and manufacturing a rotary tool, its machining parameters and their effects on surface roughness of aluminum alloy of Al99 which is one of the most consumable alloys in aerospace industry, is studied and optimized. First, the rotary tool is designed and manufactred. Then according to Taguchi method, the experiments have been designed to record surface roughness, machining temperature and exerted forces on the tool. In order to evaluate optimum condition of the experiment results, MINITAB and Genetic Programming (GP) have been implemented to obtain the best regression; then for obtaining the optimum condition of machining, the results of running Genetic Programming has been used. In the end optimum machining parameters to achieve the best surface quality is presented.