Thanks Guys
Bitlocker will not work for my case due to it's encryption on the drive level.
I'm going to configure EFS on FileStream folders based on this article https://mizitechinfo.wordpress.com/2014/07/29/step-by-step-encrypting-user-data-with-efs-in-windows-server-2012-r2/
and see how it goes.
I setup a SAN share on which FileStream is stored and will encrypt it with EFS (Windows Server 2012 R2)
I'll post my results in a few days.