A compact and stable femtosecond laser micromachining system was founded based on Yb-doped large-mode-area photonic crystal fiber (PCF) femtosecond laser amplifier, which outputs pulse with 1040 nm center wavelength, 50 MHz repetiton rate, 100 fs pulse width, 16 W maximal average power and 85 fs pulse duration after compressed by grating. Fabrication of micropatterns on silicon and metallic thin film (Cr, Al) was demonstrated by the system and the obtained micropatterns were compared with those fabricated by solid-state Ti∶sappire femtosecond laser amplifier with 1 kHz repetition rate. It shows that due to the lower and easily adjusted single pulse energy of our high repetition rate femtosecond laser, the proposed system can effectively control the morphologies of micropatterns, and avoid contamination during micromachining, herein, protect the substrates. The characteristics of high repetition rate and high average power for the founded system are revealed to be advantageous for femtosecond micromachining in aspects of improving the fabrication outcome and promoting the efficiency.