The present disclosure relates to a method and a system for marking multimedia files with file-marks and manipulating multimedia file(s) with the help of file-marks. In an embodiment, the present disclosure provides a method to link searchable keywords and tags to each of the file-marks. Each user of the multimedia file can define an index of file-marks with associated keywords and tags. The user of the multimedia file is provided with an option to play highlights created by a chosen set of users. One or more actions are initiated at the time of file-marking, associating the keywords and tags with a file-mark or at the time of manipulating the file-marked multimedia file. It also provides a method for facilitating file-marking one or more media files by one or more external file-marking device(s). Further, disclosure presents methods to efficiently encode and decode a multimedia file with highlights.