I would not clain expertise in this subject, but my understanding is filters will remove larger nasties such as bacteria, amoebas and cysts; but will let viruses pass through. If your in a region where the viral load of streams is high, you need more than a filter. Either a purifier or chemical treatment is indicated. If the viral load is low, a filter is sufficient.
Mechanical filters and purifiers both have the problem of clogging, but prefilters help.
When i have camped, I have usually been happy with a filter.