Remove a Certificate from a Microsoft Server Using the Certificate Utilty
Before deleting an old certificate make sure that either your old certificate has expired, is not being used, you are done with it (usually for Code-Signing Certificates) or that
your new SSL certificate has been thoroughly tested to make sure it works with all of the clients you're aware of before deleting the certificate.
Deleting a Certificate from a Server is fairly simple, you will just need to run the Certificate Management Utility on your server.
Then right-click and choose Delete Certificate.
You will receive a warning that the certificate will be gone for good (i.e. it's not like Window's recycle bin. There's no undo button).
After clicking 'Yes' your certificate will be deleted, and won't show up in the MMC, in IIS, in Exchange or the DigiCert Utility.
Deleting an SSL Certificate from a Windows Server Using the DigiCert Utility
Tutorial on deleting an SSL Certificate from a Microsoft Windows Server