We demonstrate that the amplitude and phase accuracy of a Fourier-domain optical processor (FDOP) can be improved by an iterative feedback technique. The spectral amplitude and phase of a periodic optical signal exiting the instrument is monitored using a linear self-referenced electric field measurement. Comparison of this measured output signal with the target waveform allows an iterative correction to be applied to the FDOP that is used to shape the amplitude and phase of the input signal. The feedback system used is capable of correcting many of the common imperfections found in these devices. Experimentally, we are able to demonstrate a factor of three improvements in both the spectral amplitude and phase accuracy of the output waveform. © 2011 IEEE.