You can follow this to remove that:
Use one txt file that contain all the users which you want to remove all the smtp addresses except primary smtp address.
Then run this script to help you remove:
$mailboxes=Get-content "C:\username.txt"| get-mailbox
$mailboxes| foreach{
$Emailaddresses=$_.Emailaddresses
for($i=0; $i -lt $Emailaddresses.count; $i++){
$Emailaddress=$Emailaddresses[$i]
if($Emailaddress.IsPrimaryAddress -eq $true){
$Emailaddresses=$Emailaddress
}
}
set-mailbox $_ -Emailaddresses $Emailaddresses
}
Thanks,
Evan
Evan Liu
TechNet Community Support
