Techniques to scan and reorganize media files to remove gaps are described. In one embodiment, an apparatus may comprise a media handling component operative to receive a media file, the media file comprising a header portion and an encoded media portion, the header portion comprising one or more indexing tables, the encoded media portion comprising a plurality of encoded chunks; a media topology component operative to build an encoded media topology list by scanning the one or more indexing tables; and a media rebuilding component operative to build the media file into a rebuilt media file by copying the plurality of encoded chunks while generating one or more replacement indexing tables where the encoded media topology list indicates that the encoded media portion contains one or more unreferenced portions. Other embodiments are described and claimed.