Sorry I have been trying to get outdoor stuff done between the rain showers. The method I have used is siphon out some of the material into a container. Stir it up. Pour it through a very fine paper towel into a clear container. Wait 30 minutes. Dinos will reform into mucus or snotty masses.
Trying to remove flagellates (protists) by filtering the water is not easy. They are generally 15 to 40 microns. Normally siphon it out of the tank and discard the water is best.
I tried all the remedies - High Ph, hydrogen peroxide, no water change (reduce silicate), 3 day blackout, freshwater, UV sterilizer, Dr Timm's, carbon dose, etc.
What I think worked! Better husbandry (Don't wait for a problem to begin to develop before doing maintenance). l siphoned out what I could from the tank/refugium and discarded the water. Started auto water changes. Did a 3 day lights out (I did not blackout the tank) and reduce the lighting schedule to 7 hours. Added a UV sterilizer and used Dr Tims Waste Away. THE SOLUTION IS TO KEEP THINGS IN BALANCED AND STABLE.