SSL Prerequisite(s):

You will have generated a CSR (Certificate Signing Request), prior to this. For an easy way to generate the EMS CSR Command, see here:

Exchange 2007 EMS CRS Command Generator: Exchange 2007 CSR
Exchange 2010 EMS CRS Command Generator: Exchange 2010 CSR

You will have Installed your Intermediate Certificate (via mmc) prior to the below.

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How to Import the SSL Certificate

From an elevated Exchange Management Shell, run the following command to import the SSL Certificate into Exchange 2007 \ 2010:

Import-ExchangeCertificate -FileData ([Byte[]]$(Get-Content -Path c:\certificates\YOUR_CERTIFICATE.cer -Encoding byte -ReadCount 0))

Note: Replace “c:\certificates\YOUR_CERTIFICATE.cer” with the path of your Certificate location

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To enable the Certificate and assign it to the relevant services, run the following command:

Assign Certificate in Exchange 2007:
Enable-ExchangeCertificate -Thumbprint *Insert Thumbprint* -Services “POP,IMAP,SMTP,IIS”

Note: replace *Insert Thumbprint* with $your_Thumbprint (you will see this in the output of the previous command).

Assign Certificate in Exchange 2010:
Enable-ExchangeCertificate -Thumbprint *Insert Thumbprint* -Services POP,IMAP,SMTP,IIS

Note: replace *Insert Thumbprint* with $your_Thumbprint (you will see this in the output of the previous command).

Original Source:
https://support.comodo.com/index.php?/Knowledgebase/Article/View/712/37/certificate-installation-exchange-2010-powershell