There are two methods to encrypt the data files (Favorites, Custom Commands)
Method: Encrypted File System (EFS)
Open Windows Explorer (explorer.exe)
Locate the application data folder. Open the Settings dialog from the menu: Tools -> Settings. It's the Application Data Folder in in the General dialog The default location is %APPDATA%\SmartFTP\Client 2.0.
Right-click on the folder and click on Properties from the context menu.
In the General tab of the Properties dialog click on the Advanced button.
In the Advanced dialog check the Encrypt contents to secure data option.
Click OK and the files will get encrypted.
Method: TrueCrypt Applies To: All operating systems