I am trying to run ASP MVC application with SSL mode set to true and whenever i run the application, i get prompt to trust the IIS Express SSL certificate. Upon clicking Yes
Note: Adding the OP's solution from the question as an answer.
This is what worked for me. deleted all localhost certificates. ran repair IIS Express in Add/Remove Programs. Copy and pasted localhost certificate from Personal/Certificate to Trusted Root Certificates and it didn't complain anymore.
Repairing/reinstalling IIS Express does not appear to actually fix this issue (as of IIS Express 10), the real solution is to add the localhost certificate to Trusted Rood Certificates.
Full details for how to do this is covered by this blog post: https://blogs.iis.net/robert_mcmurray/how-to-trust-the-iis-express-self-signed-certificate
In summary,