Starting from MIUI 6.11.10 on stock and localized ROM versions (also some custom ROM versions with custom AGNi / Radon kernels) Goodix fingerprint scanner isnt working. Below youll find a fix patch archive.
How to fix Goodix Fingerprint Scanner on Redmi Note 3 Pro Special Edition
Before installing custom kernel, youll need to download and install this patch. While installing select Goodix model. Simple as that. Just flash this Goodix FP fix before installing any custom kernels. Works on MIUI 6.11.10+ and MIUI stable V8.1.1.0 ROM.
Download Goodix FP Patch