I do not know if I understood well the technical problem, hence i apologize if my answer is inappropriate.
If this powder is polar you can use a functionalized polyolefin or EVA to compatibilize PE and the powder. Probably the powder can get stick to LDPE and be carried out from screws.
Mrs.Maria-Beatrice Coltelli I have already used LDPE and powder together but powder is stick to screws. When I use only LPDE to clean sticked material on screw, it didn't work. Powder is remain on my screw surface. Mr.Victor I will try suggestion thank you.
I am not sure what antimicrobial powder you do have, but I will do following.
If you still have that same antimicrobial filler laying around, and you do have a TGA on campus; please perform a scan and find out the decomposition temperature of your antimicrobial agent
Once you have that temperature, and if it is below 550C, then pull the screw out from the extruder. Dissemble the elements and put them in the furnace (be very careful since steel will oxidize at prolong exposure to temperature around 600C)
Once the material is decomposed, just clean the elements with brush and put the screw together
Option B would be find a solvent which will not be aggressive on elements and rather putting elements through elevated temperature exposure. Soak them in that solvent (Please consult your lab tech before doing this)
Option C I would not recommend this, because you may not get rid of the powder effectively, but if you have a glass filled PC or SAN laying around run it with the lowest recommended temperature conditions. It should help
I would use a low MI HDPE. Also, there were rubber modified film grade PE resins which have been known to scour the barrel wall and the extruder flights pretty well.