Here is a summary of the steps.
DISCLAIMER: I AM NOT RESPONSIBLE IF YOU BRICK YOUR PHONE.
1. Download and install ClockworkMod. This will give you adb.exe.
2. Download and install adb USB Drivers.
3. Download and install the LATEST version of the MiFlash tools.
4. Downloaded the CORRECT latest MIUI 8 Fastboot ROM that you want to install according to your phone model. This is a .tgz file. You will need to extract all of the files.
5. Enable Developer Options on your phone. Enable USB debugging. Plug your phone to your laptop. Accept the warning that appears on your phone.
6. Navigate to where "adb.exe" has been installed. Then run:
"adb devices"
It should show you that your device is connected.
"adb reboot edl"
Your phone screen will turn blank and the LED red light will flash slowly.
7. Run MiFlash tools, point the folder to where the .tgz was extracted in step 4, and be sure to choose the "Flash All" option on the bottom. Be aware that ALL your existing data on your phone will be deleted.
8. Choose Flash, wait for between 3 - 4 minutes, and MiFlash Tools should show success.
9. Unplug the phone from your laptop, and long press the power button to boot up.
Congratulations, you have a clean MIUI 8 installed.
DISCLAIMER: I AM NOT RESPONSIBLE IF YOU BRICK YOUR PHONE.
If you need someone to do it properly (I have done it successfully many times for more than 10 phones), I can do it for $10. You just need to come to my place and you must have the Redmi Note 3 PRO model. PM me if interested.