A media fingerprint archive system generates and archives media fingerprints from second media content portions such as commercials. A downstream media measurement system can extract/derive query fingerprints from an incoming signal, and query the media fingerprint archive system whether any of the query fingerprints matches any archived fingerprints. If so, the media measurement system can perform media measurements on a specific secondary media content portion from which the matched query fingerprint is derived. If not, the media measurement system can analyze media characteristics of a media content portion to determine whether the media content portion is a secondary media content portion and perform media measurement if needed to. The media measurement system may send fingerprints from an identified secondary media content portion to the media fingerprint archive system for storage.