First, you need to make sure that your EVO 3D has the latest software running on it which would be 2.08.651.2. If for some reason your phone isn't up to date, you can go to Settings –> System Updates –> Firmware Update to pick up the latest version of the firmware. Once you have the latest firmware on your HTC EVO 3D, head over to HTC's Dev website and follow the instructions. Just remember that there is no such thing as a free lunch. Even though HTC is giving you the tools to do this, unlocking the bootloader will void your warranty on the phone.
source: HTC via AndroidandMe
The latest firmware update for the HTC EVO 3D gives you the ability to unlock the bootloader on the phone