A fiber laser system includes a fiber mode-locking oscillator, a fiber stretcher, a multistage amplifier chain, a pulse picker, and a compressor wherein at least a device for performing a pulse shaping, a spectral shaping and a polarization shaping and a combination thereof is implemented in the fiber mode-locking oscillator, the fiber stretcher, the multistage amplifier chain, the pulse picker, and the compressor for managing and reducing nonlinear effects in the fiber laser system. The combinations of pulse shaping, spectral shaping and polarization shaping in different stages of the fiber laser system enables the fiber laser system to generate a short pulse of <200 fs and a high energy laser in a range between 1 uJ to over mJ and an average power from 1 W to 100 W.