There are many reasons why it is difficult to classify microorganisms. First of all they are so small that it takes a high powered microscope to even view them. Secondly, everything that small pretty much looks the same (for bacteria at least). Bacteria and fungi are usually classified by metabolic criteria rather than visual. Will it grow on certain media under certain conditions? Even then, more than 95% of the known bacteria in the world are unculturable under laboratory cricumstances.