Question: 

How does one import the IWA root certificate manually on the machine to enable Windows MFA?


Answer:

Download your IWA root CA certificate:
KB-7074: Why is Centrify changing IWA, what changes are being made, and how can I ensure IWA continues to work as expected post 16.7?

A video walkthrough of how to download and distribute the IWA root certificate using group policy can be viewed HERE.

Import IWA Certificate on the machine you wish to use Windows MFA at login do the following:
1) Open mmc
2) File -> Add/Remove snap-ins
3) Select certificates
4) Select manage certs for computer account -> Next
5) Local computer -> Finish
6) Ok
7) Open Certificates -> Trusted root certification Authorities -> Certificates
8) Action -> All Tasks -> Import
10) Next -> Browse for Certificate -> Next -> Finish
11) Wait for successfully imported message 

The certificate is now installed on the local machine and may successfully use MFA.