Again thanks to all who replied. I couldn't do this tonight as there was something very important on that needed to use the network. I'm going to tackle it tomorrow.
The servers are detecting the virus (even though they were right up to date with Windows updates and anti virus). When I removed it with Sophos, the server service was stopped, I ran another virus scan straight away and nothing was detected, I rebooted in safe mode and ran another scan and nothing was detected again but as soon as I rebooted normally and was connected to the network it reappeared.
There's no way I'm flattening them, so need to remove.
Going to turn everything off tomorrow, go round each workstation and run the hotfix and a virus scan. Once I've done that I'll do the same on the servers and then re-connect everything.
I'll turn autorun off so USB sticks don't spread it and then will insist any sticks get brought to myself for a scan before use.
Is this Malwarebytes Anti Malware free? I've never heard of it, but I am willing to try anything that will make life easier.
Thanks again for everyones help.