بسم الله الرحمن الرحيم
I am using honey for a long period of time and its indeed sweet in its taste and rich in its healing power, Alhamdulillah. Allah says in the Qur'an which means:
And your Rabb inspired the bees, saying: take you habitations in the mountains and in trees and in what they erect. Then eat of all fruits and follow the ways of your Rabb made easy. There comes forth from their bellies a drink of varying color wherein is healing for men. Verily in this is indeed a sign for a people who think. (Surah Nahl: 68-69)
Once when I bought honey from natural sources I found in them are some particles of natural waxes, dead bees mixed with the honey (its perfectly normal). Then I decided to filter it without causing any damage to the quality of the honey. Here I will explain you how I did it, may be useful for you later inshaAllah.
Step 1: Take a clean vessel preferably in glass otherwise steel. Make sure it its completely dry if you happen to wash it with water then let it dry for some time under sun or mild fire.
Step 2: Take a clean and thin piece of cloth that is transparent and without any minute threads coming out. These small threads may mix with honey and upset your stomach later.
Step 3: Pour the honey into the vessel and cover its mouth with the cloth. Now tie the cloth tightly around the neck of the vessel so that it does not break or leak.
Step 4: Take another clean vessel almost of same size and place it on top of a plate. Pour water in the plate, so that your honey will be protected from Ants even if you leave it unattended (automation)!
Step 5: Finally, place the loaded vessel top of the empty vessel (as shown in the picture above). Make sure you placed both the vessels in perfect gravitational balance otherwise it may fall and spill all the honey!
Just leave it in its place without any disturbance, you can see the clean drops coming out. Its slow but completely automated without any side effects! I got my honey filtered in 1 day.
Hope you found it useful.