@hanumant-sidraya Can you please clear up a few things.
It sounds like you have customers that have their own IdP. When you say "the customer has exposed the API for authentication.", what does that mean. They have an API that can confirm their identity?
If you have the APIs and authentication working with the customer's IdP, have you tried enabling the Two Factor Authentication for the user? Go to your user details screen in FusionAuth and then click 'Enable Two Factor' from the dropdown in the upper right hand corner?
For more details, you can refer to the Two Factor API documentation and the Enable Multi-Factor Authentication API documentation.