Sorry to hear about the infected Server, hopefully there's not much downtime involved, that would have been critical to a business like what you have. Hopefully you have a full backup before the infections?
The link that Corrine has provided you is very helpful, follow the advice given. Also, have a read at this Article
from Trend Micro on how to clean up the infections, I think that you would need the full version of OfficeScan-Endpoint Protection
running to follow these steps. I see they have a 30 days trial version and install it for now. Are you able to access the internet from the Server? We use McAfee Saas Endpoint Protection
and with my experience dealing with multiple Servers for me, it's the best Security server protection. You might want to check that out, they are quite reasonable. McAfee has also trial versions that you may try. I've seen a few times how McAfee Saas business protection blocking and cleaning out all virus/spyware, again this is based on my own experience dealing with few Servers in the past 12 years.
Luckily we don't get too many attacks or infections due to the Network Security protection that we've installed. You should invest on buying excellent protection for your Servers - Security Software/Hardware to protect your network. Also, a firewall/security hardware is highly recommended and it's a must for a business similar to Sonicwall. All the computers will need to have AV/Security programs installed and have the latest Windown Updates/Service Packs/Patches installed as well.
More info. in this Article
that I wrote on how to secure your network.
Hope this helps....and good luck!