A biofilter was a scanning device that analyzed an incoming transporter matter stream for known biological anomalies. When it detected such anomalies, like viruses, it attempted 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 distinguished from the matter stream by the biofilter and thus cannot be screened out. (TNG: "Realm of Fear")

While on a survey mission to Surata IV, the Enterprise's biofilter detected an unknown microorganism in William T. Riker, but could not filter it out since it had fused itself with his nervous system. (TNG: "Shades of Gray")

Biofilters were also used in replicators. However, it was possible to bypass the biofilter by reprogramming the replicator to build a virus directly into the food it created. This occurred on Deep Space 9 with the aphasia virus developed by Dekon Elig and Surmak Ren, who created a device to introduce instructions on creating the virus into a replicator's pattern generator. (DS9: "Babel")

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")

The biofilter can be reprogrammed to filter out specific molecular patterns. (TNG: "Realm of Fear", "Unnatural Selection")

In 2374, The Doctor told Romulan Commander Rekar that he checked the biofilters on the bridge of the USS Prometheus for any signs of the Terothka virus. This was an alibi used by The Doctor but was uncovered by Rekar. (VOY: "Message in a Bottle")

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