I clean filters the same as I clean eyepieces. First, use a blower to remove any particles that you can. Then I use a lense brush to gently remove any other particles that didn't get the hint with the blower brush.
At that point, most of the grit that could do damage to your filter should be gone. I make three tear drop shaped pieces of cotton wool and set them aside. I put a couple of drops of pure isopropyl alcohol on the first piece of cotton wool (on the big end, holding the small end) and clean the filter gently. I then immediately grab the second piece of cotton wool and dry the filter before the alcohol can dry out (and deposit any grime that was in solution back onto the filter). After that, I breathe on the filter, and clean the moisture off the lense with the third piece of cotton wool.
I get perfectly clean eyepieces and filters using that method. Be careful to only use a couple of drops of isopropyl though, especially on lenses. You don't want any fluid finding its way into the edge of the lense etc.
Clean your filter gently, patiently and methodically, and never re use any cotton wool and you won't go wrong.
Dean
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