In order for the UV light to be able to do its job in the SteriPEN, the light must be able to reach every corner of the container.
With clear, particle-free water this is not a problem, but if there are particles in the water, it may be possible for germs to evade the light and survive.
If you want to be on the safe side, pre-filtration is essential. A filter alone, which has no virus level, cannot eliminate viruses as SteriPEN does.