Clamwin, Avira, and AVG are some of the free AV’s out there on the market. You should look at licensing restrictions though as the license may not apply for your organization. Note that the Microsoft Malicious Software Removal Tool (MRT) is included in each monthly Windows update and is a very good tool for scanning & cleaning an infected system. It is for detection and removal only. It does not provide any active protection.
For anti-virus, I would recommend AVG.
Some other useful anti malware options:
-MS Windows Defender
You can protect your computers temporarily by preventing them to access the internet and other external storage devices. Remember that trojans and any other viruses only come from external sources mostly from the Internet and USB storage devices.