Hello Muhammad Rizwan_NRL,
Thank you for posting in Microsoft Community forum.
Based on the description, I understand you have a Windows server 2008 R2 in domain, and you have a shared folder on this server, and selected users have access rights on this shared folder, now you want to protect subfolders in this shared folder with password, am I right? If so, you can use BitLocker.
Enable BitLocker on the drive where your folder is. Though not a subfolder-specific solution, it encrypts the drive and requires a password.
Or using Third-Party Software if you need.
Always remember to keep a backup of your data in case you forget the password, or something goes wrong with the encryption process.
I hope the information above is helpful.
If you have any question or concern, please feel free to let us know.
Best Regards,
Daisy Zhou