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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 distinguished from the matter stream by the biofilter and thus cannot be screened out. (TNG: "Realm of Fear")

Biofilters are also used in replicators. The replicator biofilters on Deep Space 9 were unable to filter out the aphasia virus developed by Dekon Elig and Surmak Ren. (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")

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