There will always be microfauna in the system.  Most are harmless commensals that  just eat leftover organic waste.

Treatment is difficult, and adding chemicals can harm beneficial balance of microorganisms and fish.   You should seek fish veterinary consult.  If it is not a confirmed fish pathogen, I would ignore it.  

Thank you for your reply Elizabeth. I also think I may be overreacting. If you have experience in treatment/chemicals though, please do share. However, I also think vet consultation would be a requirement before trying any of the chemicals.

You can ask Techniplast for advice also.

I tested the zebrafish system with methylene blue(1ppm) for 24 hours without new water. This treatment did not change pH, nitrate, nitrite and production of zebrafish.

But I don't know how much effective it did. I hope it help you for disinfection.

Elisabeth's advice is an important first step because is you really want to sterilize your system it would involve removing the fish, possibly disassembling the system, scrubbing off any biofilm and treating with something like bleach. The biofilter would then have to be re-established before the fish are returned to the water system. Not something I would want to start based on a possibly wrong assumption.

Details of best cleaning approaches could be obtained from Techniplast.

Dis-assembly of the system might be required in case nematode eggs were splashed up out of the water were merely adding of chemicals to the circulating water might not might not get to them and kill them.

Methylene blue would be expected to kill or negatively impact the functioning of your biofilter because its anti-bacteria activities.

Thank you for all the replies. @Bill yes I know the whole process and would rather avoid that. But as you said, just merely adding a chemical may not completely remove the eggs and may affect the biofilter/fish. @Jae-Ho I do add methlyn blue into my embryonic E3 media but not into the system. Perhpas it should be avoided for systems with biofilms.