@Mahendervyas35821
As far as the initial configuration of the Microsoft CA server is concerned there isn't anything special required related to ISE.
You just need the CA installed and configured, you'll require the Trusted Root Certificate deployed to all AD joined computers, this can be done using GPO.
Examples:
https://social.technet.microsoft.com/wiki/contents/articles/15037.ad-cs-step-by-step-guide-two-tier-pki-hierarchy-deployment.aspx
https://www.virtuallyboring.com/setup-microsoft-active-directory-certificate-services-ad-cs/
You will also need to install the Microsoft CA Web Enrollment GUI, to be able to sign CSR (Certificate Signing Requests) from ISE.
You will need to import the CA Root Certificate and import into ISE's Trusted Root Certificate store.
Optional - If you require SCEP or are going to use pxGrid, then you would need to tweak the CA configuration, refer to this post.
http://www.network-node.com/blog/2015/12/24/server-2012-configuration-certificate-templates?rq=ise