A Biofilter is an scanning device which scans an incoming transporter matter stream for known biological anomalies. When it detect such anomalies, like viruses, it will try to remove them from the stream. The transporter operator will always be warned when the biofilter can or cannot removes biological anomalies. The exception is that when microbes exists as matter and energy the biofilter cannot filter them out because it cannot distinguish them from matter stream.
After Deanna Troi, Miles O'Brien and Data were taken over my Ux-Mal criminals, the biofilter scans showed that their nervous systems were generating high levels of synaptic and anionic energy. (TNG: "Power Play")
The biofilter can be scanned for specific molecular patterns and reprogrammed to filter them out. (TNG:"Realm of Fear")