Computer File Systems are far more complex than just a persistent storage device for files and folders. Features such as hard & soft links, alternate data streams, and security integrity are very useful to the operating system, advanced applications and user convenience. However, these can often be hard for users to manage and understand using standard tools. Disk Spectra is a tool designed with an intuitive user interface that provides very detailed information about file system contents, and easy to use tools for managing advanced file system features. The application displays and manages file & folder details such as volume layout, precise space usage, hard & soft links, object IDs, quotas, fragmentation, data streams, security settings including integrity, and free space contents. Users can defragment individual files & folders, clear (erase) data from free space, create & delete links and data streams, extract data from alternate data streams, set security integrity, determine where disk space is really being used, and easily identify differences between actual space used and file sizes or quota amounts. A command line tool is also provided for running lengthy or off-hour operations using the task scheduler.