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Source: Microsoft Support
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In Windows 2008, when you duplicate a template, you have an option to select the minimum supported CA. (Windows 2003 Enterprise or Windows 2008). If you want to use Web Enrollment to request the certificate based on a Custom Template created in the Certificate Authority running on Windows 2008, then you would have to create the custom template with Minimum supported CA as Windows 2003 Enterprise.
To Publish a Custom Certificate via Web Enrollment, we need to do the following.
Go to Run and type certtmpl.msc which will open the certificate template manager.
Create a Duplicate Template of the available templates from Certificate Template Manager by right click the existing template and select Duplicate Template. Select Windows 2003 Enterprise as Minimum Supported CA.
Edit the Copy of the Template certificate template by viewing the Properties. You can provide a custom Name, validity and select "Publish certificate in Active Directory"
On the Security tab, select Authenticated Users and click to select the Allow for Read and Enroll check box. You can also use a custom security group to whome you want to give this functionality.
On the Request Handling tab, place a check next to Allow private key to be exported.
On the Subject Name tab, click the radio button which states Supply in the request.
Go to the Certificate Authority Snap in and right-click Certificate Templates folder. Point to New and then click Certificate Template to Issue.
Select the new custom template and click OK.
Restart the CA service.
From the server which needs the certificate open the web page http://servername/certsrv and do a Advance Certificate Request. The custom V2 certificate template should be available in the drop dow now.
Enter the FQDN of the server getting the certificate as the Subject.
Make sure the certificate private key is exportable and complete the request.
Templates Created for Windows 2008 Minimum CA level cannot be used for Web Enrollment
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