I dont understand what you are asking. The ceramic media is housing beneficial nitrifying bacteria, if you remove them you need to make sure you have enough media/rock to continue to support the cycle of your tank.
Unless you were running this canister filter as a nitrtate reactor and it reached saturation, removing this media will not reduce nitrates. The "nitrate factory" is a myth, once organics is broken down to nitrates, thats the end, they do not reproduce. Removing organics either through a skimmer or cleaning the mechanical filtration of trapped organics will decrease nitrates.
Cyano is more likely caused by too high of phosphates in relationship to nitrtates, rather than too high nittrates.