Methods and systems for creating, reading, and writing compressed files in a computer system comprising a file system coupled with storage medium and at least one application program interface (API) configured to communicate with the file system by means of file access-related requests are provided. The file access-related requests are intercepted in order to provide at least one of the following: a) to derive and compress data corresponding to the intercepted file access request and to facilitate storing the compressed data at the storage medium as a compressed file; b) to facilitate restoring at least part of compressed data corresponding to the intercepted file request and communicating the resulting data through the API. The compressed files comprise plurality of compressed units. One or more corresponding compressed units may be read and/or updated with no need of restoring the entire file while maintaining de-fragmented structure of the compressed file.