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A biofilter is a scanning device that analyzes an incoming transporter matter stream for known biological anomalies. When it detects such anomalies, like viruses, it will attempt to remove them from the stream. The transporter operator will always be warned of detected anomalies whether or not they were able to be removed. Of note, microbes that exist as both matter and energy cannot be distinguish them from matter stream by the biofilter and thus cannot be screened out. (TNG: "Realm of Fear")
After Deanna Troi, Miles O'Brien and Data were taken over by Ux-Mal criminals, the biofilter scans showed that their nervous systems were generating high levels of synaptic and anionic energy. (TNG: "Power Play")