Early October 2008 an email was received on my system with the subject: [NO REPLY] UPS Tracking Number followed by 8 digits. Included was an attached file UPS_letter.zip As I was away my wife opened this believing I had a package coming from UPS.
The computer runs Ubuntu 8.04, the e mailer is Thunderbird 2.0.0.21 and hasn't been used since, as its obviously the UPS Trojan. I now want to use this machine. It was being run as an ordinary user, not as root.
My understanding from reading the publically available information is that this Trojan is only a windows one, and that the structure and safeguards in Linux will prevent it from damaging my system and propagating elsewhere on the web.
An I correct, if not what next?

Trend Micro's page for this trojan doesn't list GNU/Linux as an affected platform. In addition, the descriptions I've read on the Web would support the theory that this is strictly Windows-only. Normally, this would inhibit the malicious actions of said programs to the point where GNU/Linux security features wouldn't come into play, since the payload wouldn't be properly delivered in the first place. If you're still concerned, you could backup your wife's documents and nuke her account (then create a new one for her).

Many thanks for confirming what I thought was the case, I should learn more of the detail of Linux instead of just using it.