There isn't one command that you can run which will easily clean up all the already-deleted files for you. However, there are a number of things you can do to reduce your vulnerability to this sort of attack in future.

As others have said, using tools like shred or srm allows you to delete a specific file by actually overwriting it, rather than just removing it from the filesystem. If you're feeling bold, you can replace the rm command with shred or srm to securely delete files going forward. That means that whenever you (or another program) tries to delete something using rm, the secure delete command will run instead.

However, if you're using a solid state disk, or even some newer mechanical disks, shred and other overwriting-based methods may not be effective, since the disk may not actually write where you think it's writing (source).

Full-Disk Encryption

A more convenient option is full-disk encryption. If you use the alternate installer, Ubuntu can automatically set up a fully-encrypted disk for you you, but you can also customize and configure the settings yourself. Once installed, the encryption is almost invisible to you: after you enter the passphrase (be sure to pick a good, long one) when the computer starts up, everything looks and feels just like normal Ubuntu.

You can also encrypt external media like USB drives using Ubuntu's Disk Utility. Setting up an encrypted external disk is as simple as checking the "encrypt underlying filesystem" box when formatting the disk. You can even store the passphrase on your (encrypted) keyring, so that you don't need to enter the phrase every time you plug that disk into your computer.

If your whole disk -- and all your removable media -- is encrypted, there's much less to worry about. A thief or police officer would need to swipe your computer while it's on, (or within a minute or two of turning it off if they're very good) in order to access your data. If you hibernate (rather than suspend) your computer when it's not in use, then you should be pretty safe.

If you ever need to completely destroy all your data, you don't need to do a Gutmann wipe of your whole disk. Simply overwrite the very beginning of the disk, to destroy the headers for the encrypted volume. Unlike with a regular filesystem, this will actually make it impossible to recover the data.

So, how do you go from your current setup to a safely encrypted disk? It's quite a challenge to retrofit a currently-installed operating system to use an encrypted disk. The easiest approach is to backup all your data and settings, then reinstall with an encrypted disk. When backing up, make sure to back up your data to an encrypted external drive, but don't save the passphrase in your keyring.

After you've backed everything up, you may want to aggressively wipe your hard drive, to make sure that none of your existing data can be recovered in the future. If you're using an SSD, the process is even more challenging, so depending how much you want to invest in the process, it might be worth destroying your current disk (a challenging proposition) and starting with a new one.

When reinstalling the OS, if you haven't aggressively wiped the disk already, you should make sure to completely fill the new encrypted partition, which will overwrite all your old data. Once you've restored your backup, you may want to aggressively wipe the start of the backup disk, to destroy the encryption header, so that it can't be recovered again.

Update: If you have not yet deleted the file that you want to be non-recoverable, use the accepted answer. If, however, you already deleted the file[s], then this is the next best method that I know of.

If I read you right, you want to erase all your previously deleted files. Here is a simple way to do that:

$ dd if=/dev/zero of=/path/to/mounted/partition/tmp_file bs=1M count=999999999999

Let that run till it complains till it gets a disk write error [out of space]. Then delete the file! What this does is just fill up your empty disk with 000s, so all your previous files get overwritten. Make sure to delete the file now, or you will not have any disk left. You might want to do this a few times if you are really paranoid. Or if you want to write random to your disk, I'd suggest replace /dev/zero with /dev/urandom.

However, this will take much much longer, so I'd run it overnight. Also, if you want a progress meter, do this instead:

$ free=$( df {PARTITION OR MOUNTPOINT}  |awk '{print $3}'|tail -1 )
$ dd if=/dev/zero bs=1M count=999999999999 | pv -s "$free" > /path/to/mounted/partition/tmp_file

First you are getting your free disk space with du, awk, and tail, then using dd to get /dev/zero, piping that to pv which stands for "pipe viewer", that redirects everything to tmp_file Once again, delete the file afterwards. $ rm tmp_file

Anyway, hope someone finds this useful! :)

First, delete files with rm on the terminal or with shift-delete on nautilus. Better yet, use srm, from the Secure-Delete tools package.

You can install the secure delete tools like this:

apt-get install secure-delete

Second, use sfill to wipe out unused space on your disk:

sudo sfill -f <directory>

This will take some time, since it is using crypto techniques to fill out the disk.

Warning: this is going through your whole filesystem, and you are root. Use with care!

This will create a file which wipes out all previously existing data. The file will be created in <directory>.

A GUI program for this is BleachBit (it's also in the sources). More recent (deb file) version at the BleachBit Sourceforge page.

Beyond simply deleting files, it includes advanced features such as shredding files to prevent recovery, wiping free disk space to hide traces of files deleted by other applications.

"BleachBit quickly frees disk space and tirelessly guards your privacy. Free cache, delete cookies, clear Internet history, shred temporary files, delete logs, and discard junk you didn't know was there. Designed for Linux and Windows systems, it wipes clean 90 applications including Firefox (vacuuming to make it faster), Internet Explorer, Adobe Flash, Google Chrome, Opera, Safari and more." (from )

BleachBit has several advanced cleaners:

• Clear the memory and swap on Linux
• Delete broken shortcuts on Linux
• Delete the Firefox URL history without deleting the whole file—with optional shredding
• Find widely-scatted junk such as Thumbs.db and .DS_Store files.
• Delete the OpenOffice.org recent documents list without deleting the whole Common.xcu file
• Overwrite free disk space to hide previously files
• Vacuum Firefox, Google Chrome, Liferea, Thunderbird, and Yum databases: shrink files without removing data to save space and improve speed
• Surgically remove private information from .ini and JSON configuration files with deleting the whole file

For details on how to use Bleachbit to delete securely specific files and folders see this answer.

If you want a solution which can't be thwarted by a pathologically obsessed individual then you should consider some combination (limited by monetary resources) of:

• degaussing -- magnetically erasing the hard drive
• physically disabling the hard drive -- i.e. industrial hole punch
• acid bath <-- you can't get bits from a pile of goo.

These solutions range drastically in cost & ingenuity. A few:

For SSDs and other flash storage media

SSDs and many other flash storage media use a technique called “wear levelling” that reassigns unused blocks of storage cells based on their number of previous write cycles to prolong the drive’s life time. As a consequence, overwriting block ranges doesn’t work as a method to erase storage content securely (or even efficiently) like it does for hard disk drives. On the other hand, flash storage allows much faster and efficient secure erasure of blocks, block ranges, or entire drives.