Based on the comparison of traditional laser and fiber laser cutting system, a fiber laser based micro-machining system is designed. The main modules of the micro-machining system and the key techniques are analyzed and the corresponding solution is proposed. In particular, the driving, control and modulation system are focused on, in which an SOC system is built up, and the corresponding hardware and software are described in detail. The pulse width and frequency modulation are achieved with software, by setting the related parameters via keyboard. The power, pulse length and pulse frequency can be tunable in our modulation system, which can meet the different laser requirement in various kinds of stents cutting and micro-machining.