Hi,
I didn't find an official article with detailed step-by-step instructions for Exchange 2016. But you can find the general steps covered in:
https://technet.microsoft.com/en-us/library/dn626158(v=exchg.150).aspx.
1.As per my expericen, to configure S/MIME on Exchange on-premises, the following steps should be taken:
2.Install and configure a Windows Enterprise CA for use.
3.Export the trusted root CA certificate to a SST file
4.Set up virtual certificate collection to validate S/MIME with this SST file
https://technet.microsoft.com/en-us/library/dn626155(v=exchg.150).aspx
5.
Create a certificate templet for S/MIME
6.Users request the certificates from CA and install certificate on their clients.
7.Sign in Outlook Web App and Outlook to test S/MIME
Here is an official blog about how to configure S/MIME for Exchange Online:
https://blogs.technet.microsoft.com/exchange/2014/12/15/how-to-configure-smime-in-office-365/. The steps are slightly different. You can refer to it still for on-premises Exchange. If you have any update, please let us know.
Regards,
Alex
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