In this study, a technique for the optimization of the optical characteristics of multi-channel filters after fabrication is proposed. The multi-channel filter under consideration is based on a Si photonic crystal (PhC), tunable liquid crystal and opto-fluidic technologies. By filling air grooves in the one-dimensional, Si-Air PhC with a nematic liquid crystal, an efficiently coupled multi-channel filter can be realised in which a wide stop band is used for channel separation over a wide frequency range. By selectively tuning the refractive index in various coupled cavities, continuous individual tuning of the central channel (or edge channels) up to 25% of the total channel spacing is demonstrated. To our knowledge, this is the first report on the electro-optical solution for the compensation of fabrication tolerances in an integrated platform.