Enterprise customers can now opt for encrypted data at rest. This feature is currently only available to Enteprise hosting plans, and at an added cost. Contact sales for more information.
Data-at-rest (DaR) encryption is transparent to all end users and happens on the fly with all uploads and downloads. The feature uses an encrypted file system and at no point during the process of uploading a file is any temporary unencrypted copy stored on our server hard drives. Beware of other implementations that involve "post upload encryption" via a script.
Even though FTP Today's privacy policy assures that no technical staff will view or open any of your files (unless expressly directed to by you), the DaR feature provides added assurance that no one with command line access can view unencrypted data.