Very much depends on what you're setting out to capture in that filter!!

The risk assessment is not really different from that overarching RA that deals with the broader quarantine issues of the animal, their bedding, extra etc. Just because its a big lump of filter in a metals frame doesn't create additional hazards unless you drop it on your toe. Fumigate it - THAT process will breed control and a RA - then get an expert to remove it. Bag it and consign it to incineration 18 02 whatever. The replacement filter should be fitted by a competent engineer and tested for performance. I'm surprised, actually I'm horrified that you need help with this. It is as central a procedure to animal welfare and quarantine that if you don't know, how on earth did you get regulatory approval to operate a quarantine service? By contrast, if its just your own quarantine system, perhaps for a breeding unit or other commercial activity then regulation may not be an issue, but if you can't get the maintenance and management of your filtration system sorted then you're not providing effective quarantine and you may as well give up. Best approach now, assuming your absolutely sure that you're not going to be responsible for an NDV outbreak or whatever, then call in the ventilation/filtration engineer and ask them for help, including help with the process of in situ sterilisation. If you have a license for the provision or undertaking of quarantine services, please do contact the licensing body and explain your situation. It will be less painful for you than them finding out the hard way.