Usually, the water that I am drinking from has been pretty clear so I have not needed to prefilter any 'floaties' from the water. I take the entire cap off the Nalgene bottle exposing the wide mouth, dip the bottle in the water source, put the steri pen in the bottle, then after it has done its thing I put the cap cap back on the bottle and drink from the smaller end of the cap cap or if I have a water bladder I pour from the smaller opening that I would drink from into the bladder. I repeat this process until the bladder is filled with clean drinking water then fill my Nalgene with clean water and I am good to go. This way contaminated water never touches what I drink from. I hope that makes sense.