Like bsmith I use a separate cup to fill the bottle, then I swirl the bottle during use to insure that everything in the bottle gets a dose (all the water above the waterline. Like Doug, I then use a small amount of the clean water to flush the areas where contaminated water might have gotten on it.

I like the SteriPen very much when I am in an area with lots of water. I use it canoeing all the time. Use a prefilter in dirty water. In dry areas it takes a while to make lots of water so I use a filter. In areas where the threat levels are high (outside the US) I use a dual method. Filter and chem, filter and pen, etc.

I also like it when traveling in places where the water is suspect. I use my own bottle for washing my teeth and make drinking water in my hotel room. It is much easier than the filter I used for years for this purpose.

Respectfully,

Jerry