A microfabrication system with the use of a femtosecond laser was designed for 3D processing of industrially important materials. The system includes a 120 fs, 1 kHz laser; beam delivery and focusing system, systems for automated 3D target motion and real-time imaging of the sample placed in a vacuum chamber. The first tests of the system on the processing of stainless steel and silicon are presented. We established thresholds and regimes of ablation for both materials. It was found that at relatively low laser fluences I < 3-5 J/cm2 the regime of “gentle” ablation takes place, which is characterized by exceptional quality of the ablated surface, but slow ablation rate (< 25 nm/pulse). This regime is especially efficient for the patterning of markers on steel or silicon surfaces. The “fast” ablation regime at I > 10 J/cm2 provides much higher ablation rate of 30-100 nm/pulse, giving an opportunity of fast high-quality processing of materials. This regime is well suited for drilling of through holes and fast cutting of materials. However, it was found that fast ablation regime imposes additional requirements on the quality of delivery and focusing of the laser beam because of the presence of parasitic ablation around the main spot on the tail of the radiation intensity distribution. As industrial machining examples, we demonstrate heat-affected-zone free drilling of through holes in a 50 μm thick stainless steel foil and cutting of a 50 μm thick Si wafer with a net cutting speed of 8 μm/sec.