If you want to handle it from the server-side, you need a Virus scanning product specifically made for Exchange.
In the short term, you can try TrendMicro's Active-X based scanner for Exchange. It runs from the web. You might have to move the server outside your firewall to get it to run.
I was hit with the lovebug virus about a month ago- it took me two days to clean off everyones machine. It was a pain! But, it was a blessing in disguise. After we got hit I purchased scan mail. You can download a free full version for 30 days and it will detect / clean viruses. It checks all mailboxes and attachments for viruses.
When I got hit with lovebug virus I downloaded the trial version and installed it on my exchange server, ran it and got the fixes for the virus. Even if you don't purchase it - it is worth the 30 day free trial. But I guarantee you that after you start using it you will want to purchase it!!
You can stop any (or all) email attachments from being sent or recieved - or be extension specific (exe, bat etc.,). It is very easy to use. The best part of the scanmail feature is that it scans the mail BEFORE it gets put in the users mailbox (while it is in the send or recieve queue).
goto Microsoft.com and search for Exmerge. This will allow you to scan your priv for known virus attachments by header or attachments, you could then extract them. It will also allow you to extract mail accounts to .pst files for archiving if needed.
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