It is a mistake to be too preoccupied with cleanliness where fish tanks are concerned.  Your aquarium, once it is up and running, and fully cycled, functions like a self-contained eco-system: the bacteria in the filter (and, to a lesser degree, in the substrate and on any ornamentation) keeps the water healthy, and should be disturbed as little as possible.  So long as you do regular partial water changes, and very occasionally maintain the mechanical filtration, by rinsing it with tank water (never water straight from the tap!) whenever it gets too physically gunked up to function properly, your fishes’ environment will pretty much look after itself.