Hello,
Boxcryptor is not designed to be used to encrypt an entire hard drive but rather specific parts of your file sytem (e.g. a cloud storage folder, network share or any other folder on your computer). If you try to encrypt e.g. Windows system files, you will likely break your operating system.
If you're looking for a full disk encryption software, please take a look at Bitlocker or VeraCrypt.
Best regards,
Robert