I just had to resolve very similar problem with someone's laptop about a week ago. There are 2 options available to you at the moment (unless somebody can suggest anything else):
1. Create or download bootable "rescue" CD and do a full scan of your system drive with anti-virus.
2. Disconnect you hard drive, connect it as a slave device to a clean machine (or put it in external enclosure and connect via USB/FireWire/eSATA) and again do a full scan of your system drive with anti-virus programme.
I used Kaspersky Rescue Disk that can be "created" by installed Kaspersky Anti-Virus or Kaspersky Internet Security.
Here is a small list of other available CDs:
FREE Bootable AntiVirus Rescue CDs Download List
I personally would go with Avira AntiVir Rescue System:
Virus removal, boot sector repair, system check - free tools download
After you clean or remove infected system file that prevents your operating system from booting you should be able to boot. In my case it was infected atapi.sys as far as I remember but obviously it can be different in your case. Also the whole lot of other files was cured and/or removed. Don't feel safe though, the system is most probably still compromised and needs further scans with different anti-virus and anti-malware programmes. Basically, you again have 2 options here:
1. Save all your data (documents, e-mails (if you use e-mail client such as Outlook, Outlook Express, Mozilla Thunderbird etc.) pictures, music etc.) on external hard drive or burn that on CDs/DVDs and then reinstall operating system with full reformat. Then update the system, install anti-virus software and move all personal data back.
2. Boot into Safe Mode with Networking and start downloading, installing, updating and scanning with anti-malware programmes (Malwarebytes' Anti-Malware, SUPERAntiSpyware, Spybot Search&Destroy), going through the list of Sturtup items, analysing HijackThis log etc.
I personally would go with option 1 as this is sometimes faster and safer and guarantee that the system is 100% clean. Had to choose option 2 with that computer I was fixing though as Windows installation disc wasn't available and system restore partition was not present.