Nowadays, the virtual manufacturing is proved to be the promising technology to design a completely digital feed drive system. Especially, the initial parameters tuning, tests, error prediction and diagnostics at the actual location of the feed drive system are at a risk of stressing and even damaging the machine tool. This paper presents an analytical identification method of feed drive system based on HILS (Hardware-In-Loop System), allowing a real CNC to be prototyped quickly from standard library functions for feed drive control laws. The main purpose of drive identification outside the CNC is that it may not be performed when the drive is installed in the CNC and user has no access to the internal control structure. So, it is proposed to identify it outside CNC in the proposed HILS on the basis of a comparison of the real object and its nominal dynamic model. The rapid prototyping model can be easily executed for initial parameters tuning, testing and the risk of stressing and damaging the machine tool during the diagnosis can be avoided effectively as well. The methodology is quite general and applicable to linear or ball screw drives, controlled with commonly used controllers. Furthermore, additional CNC modules can easily be prototyped and integrated to this prototype for other research purposes. Experiments were carried out to compare HILS prototyping to the actual CNC systems. The result demonstrates that the real-time feed drive system can be accurately represented by the identified prototype model.