A fiber amplifier system including a plurality of optical components in an amplification chain that are responsive to a seed beam and that cause frequency modulation (FM) to amplitude modulation (AM) conversion to the seed beam that creates a non-uniform spectral transmission having a transmission function, where one of the optical components is a fiber amplifier generating an amplified output beam. A programmable spectral filter is controlled to pre-distort the seed beam by applying an inverse of the transmission function that creates a net uniform transmission function by equalizing a net spectral transmission profile of the seed beam at an end of the amplification chain to reduce the amplitude modulation.