In an aggregated file system, a method of processing a user file retrieves user file metadata and user data from a metadata server and applies operations to the user data in accordance with a file open request from a client. At the end of the process, the method stores the processed user data at a location in accordance with a predefined rule and updates the metadata in the metadata server to reference the processed user data at the location. In some embodiments, the predefined rule is to choose a location between the metadata server and a separate storage server in accordance with the size of the processed user data. If the size is still smaller than a predetermined threshold, the user data is stored in the metadata server. Otherwise, the user data is stored in the storage server.