Most fuel contaminants are heavier than fuel and will settle to the fuel tank bottom if undisturbed. To remove this contamination it is best to remove free and emulsified water and filter the contents in the lower 5%-15% of the tank. This process will keep from mixing the clean fuel with the contaminated fuel.
Tank cleaning is a relative term. A clean tank should be able to store fuel in a condition that exceeds the engine manufacturer’s recommended ISO 18/16/13 cleanliness target.
Fuel should be delivered to an engine with less than 100 parts per million of free or emulsified water.
Most fuel storage tanks do not have a protective coating on the inside; only raw metal with tiny pores that become home to fungi and acidic bacteria when any moisture is present. This contamination will become a problem if you use a biocide in your fuel. When the microbes die from the biocides they fall from the tank walls in a talcum powder-like substance that can clog filters for many weeks until all microbes have been killed.
The most damaging fungi and bacteria problem is found floating at the fuel/water interface at the storage tank bottom. This contamination can easily be ingested into your engine’s fuel pickup tube, clog your filters and stop your engine.
Removing tank bottom water and the interface microbes will eliminate 98% of filter clogging problems.