To encrypt a file or files in a folder, just right-click the file(s) and select "encrypt"

Viper FTP provides high secure AES-256 encryption in CBC mode of single files using password. You simply right-click the file(s) you want to encrypt or decrypt in the file listing and enter your password in a dialog box. A new encrypted or decrypted version of the file is created.

By default the output file is saved to the same folder as the source file. To change the output folder click 'Browse" and select the folder. To replace the source file by the output one select "Overwrite source file' - your oryginal file will be overwritten.
Encrypting and Decrypting Files
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Viper FTP User Guide