There is a big risk in running a system which has been infected and "has" been cleaned of viruses. A lot of the modern trojans have routines programmed into them which allows the download of additional malware. Sometimes programmers of other viruses even use backdoors opened by malware to spread their trojans.
If you are using your computer for anything else than simple internet surfing (Which you do as you have logged onto this site). I highly recommend you format your hard drive. If you use eBay, Amazon, online banking or share your passwords and usernames on many sites this is IMO a risk I wouldn't take. Your computer may have been infected by a rootkit already which is undetectable by software installed on your computer.
Even if you are using a live cd to scan your system you may have a virus the system does not find. Backup your data and do yourself a favor and install a new virus free system. If you have backups (which you probably haven't) this should take less than two hours.