Structured document files, such as those utilized by standard productivity applications or for portable documents can have malicious computer executable instructions embedded within them. Modifications to such files can prevent the execution of such malware. Modifications can operate at a file sector level, such as either fragmenting or defragmenting the file, or they can operate at a file record level, such as removing records, adding records, or rearranging the order of records. Other modifications include writing random data into records deemed likely to have malware, removing unaccounted for space, or removing records that are not known to be good and are inordinately large. A scan of the structured document file can identify relevant information and inform the selection of the modifications to be applied.