Hardware disk encryption is completely transparent to the operating system and, consequently, to applications and users on the computer. This means saving a part of unstructured data on the disk is easy and needs no modification to the operating system, the application, or the content format.
Some kind of authentication needs to take a place before any data on the drive can be decrypted and read. When complete disk encryption is implemented using software, the operating system must have some kind of unencrypted partition from which to boot and in turn authenticate the system to obtain access to the cryptographic keys to decrypt the main encrypted disks.
Both hardware and software techniques provide the encryption of data as it is written to disk over the complete disk. The methods are completely transparent to the processes (other than, of course, those in the operating system that may be managing the encryption/decryption), and as data is read from disk, it is recognized by applications in its decrypted state. One downside of hardware-based disk encryption is that the management of the cryptographic keys can be hard.
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