A fiber amplifier system (100, 106) comprising: at least one optical source (MO 12) configured to provide at least one optical seed beam (14, 134); a plurality of optical components (20, 22) in an amplification chain and being responsive to the seed beam, wherein one of the optical components (20, 22) is at least one fiber amplifier responsive to the seed beam and configured to generate an amplified output beam of the seed beam, and wherein one or more of the optical components (20, 22) are configured to cause frequency modulation FM, to amplitude modulation, AM, conversion to the seed beam causing amplitude modulation that creates a non-uniform spectral transmission of the seed beam having a transmission function; a programmable spectral filter provided within the amplification chain and being configured to pre-distort the seed beam (14, 134) 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 (14, 134) at an end of the amplification chain to reduce the amplitude modulation; a beam sampler responsive to the amplified output beam that is configured to provide a sample beam; a detector sub-system (34, 44) responsive to the sample beam, said amplifier system being characterized in that: said detector sub-system (34, 44) is configured to detect an amount of the amplitude modulation on the seed beam, said detector sub-system (34, 44) being configured to generate a control metric signal identifying the amount of amplitude modulation; and a controller responsive to the control metric signal from the detector sub-system (34, 44) and configured to control the programmable spectral filter to generate the inverse of the transmission function. at least one optical source (MO 12) configured to provide at least one optical seed beam (14, 134); a plurality of optical components (20, 22) in an amplification chain and being responsive to the seed beam, wherein one of the optical components (20, 22) is at least one fiber amplifier responsive to the seed beam and configured to generate an amplified output beam of the seed beam, and wherein one or more of the optical components (20, 22) are configured to cause frequency modulation FM, to amplitude modulation, AM, conversion to the seed beam causing amplitude modulation that creates a non-uniform spectral transmission of the seed beam having a transmission function; a programmable spectral filter provided within the amplification chain and being configured to pre-distort the seed beam (14, 134) 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 (14, 134) at an end of the amplification chain to reduce the amplitude modulation; a beam sampler responsive to the amplified output beam that is configured to provide a sample beam; a detector sub-system (34, 44) responsive to the sample beam, said amplifier system being characterized in that: said detector sub-system (34, 44) is configured to detect an amount of the amplitude modulation on the seed beam, said detector sub-system (34, 44) being configured to generate a control metric signal identifying the amount of amplitude modulation; and a controller responsive to the control metric signal from the detector sub-system (34, 44) and configured to control the programmable spectral filter to generate the inverse of the transmission function. said detector sub-system (34, 44) is configured to detect an amount of the amplitude modulation on the seed beam, said detector sub-system (34, 44) being configured to generate a control metric signal identifying the amount of amplitude modulation; and a controller responsive to the control metric signal from the detector sub-system (34, 44) and configured to control the programmable spectral filter to generate the inverse of the transmission function.