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 isn’t working. Below you’ll find a fix patch archive.
How to fix Goodix Fingerprint Scanner on Redmi Note 3 Pro Special Edition
Before installing custom kernel, you’ll 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 V126.96.36.199 ROM.