Citric acid will clean the entire system and remove the accumulated rust.

However, the heat offered by the heater core is usually sufficient despite the condition of the cooling system. It doesn't make a lot of sense to do a citric acid flush for the benefit of the heater core. If you have overheating problems and suspect accumulated rust in the block and corrosion inside the radiator, then the procedure makes some sense.

It's not a panacea, however. Sometimes the components need replacement and the citric acid simply won't cure the problem.