BestInternetSecurity.net

If your system has contracted virus and you’ve found that you cannot boot up the system correctly or the virus is attached to a system running program that you cannot remove, then you might need to start your computer in safe mode and run a virus scan.

By operating your computer in safe mode, you are launching your system with all non-essential processes and programs disabled. Chances are now you can remove those viruses attached to your system programs because they are idle in safe mode.

Here are the steps adapted from http://articles.winferno.com/antivirus/virus-scan-in-safe-mode/
To run a virus scan in safe mode, you must have an active anti-virus software installed on your computer.
To run a virus scan in safe mode, follow these steps:
1. Restart your computer
2. Immediately after you power on your computer, repeatedly press the [F8] key for a number of times
3. In the Windows Advanced Options Menu screen, use the arrows to select Safe Mode and press [Enter]
4. Select your current operating system and press [Enter]
5. Select the user you would like to log-in under (if applicable)
6. When your system finishes booting, click the Start button on your task bar
7. Move your cursor over All Programs and navigate to your anti-virus program
8. Click on your anti-virus program to run it and follow the anti-virus program’s normal steps to run a virus scan
9. After the virus scan is complete, Delete all detected viruses
10. Close out of your anti-virus software
11. Restart your computer (it should start in normal mode)

Remarks:
To make sure the above process gets the maximum benefits, it is even recommended to turn off System Restore in Windows BEFORE you initiate a safe mode scan:

Windows XP:
Manual steps to turn off or turn on System Restore in Windows XP
(Ref: http://support.microsoft.com/kb/310405)
Steps to turn off System Restore
1. Click Start, right-click My Computer, and then click Properties.
2. In the System Properties dialog box, click the System Restore tab.
3. Click to select the Turn off System Restore check box. Or, click to select the Turn off System Restore on all drives check box.
4. Click OK.
5. When you receive the following message, click Yes to confirm that you want to turn off System Restore:

After you have done your virus removal, remember to turn on the system restore again.

Steps to turn on System Restore
1. Click Start, right-click My Computer, and then click Properties.
2. In the System Properties dialog box, click the System Restore tab.
3. Click to clear the Turn off System Restore check box. Or, click the Turn off System Restore on all drives check box.
4. Click OK.

Windows Vista:
To turn System Protection on or off for a particular disk in Windows Vista:
Ref: http://windowshelp.microsoft.com/Windows/en-US/help/f0688925-5abe-4caf-b49a-018f8cfcaf4d1033.mspx#E3

1. Open System by clicking the Start button , clicking Control Panel, clicking System and Maintenance, and then clicking System.
2. In the left pane, click System Protection .If you are prompted for an administrator password or confirmation, type the password or provide confirmation.
3. To turn on System Protection for a hard disk, select the check box next to the disk, and then click OK.
– or –
To turn off System Protection for a hard disk, clear the check box next to the disk, and then click OK.

Note:
Some anti-virus programs support boot time scan. If you have anti-virus program that supports this feature, you can schedule a boot-time scan instead of the manual safe-mode scanning.

Here is an article talking how to do this under Avast (a free anti-virus program)
http://www.techiecorner.com/166/avast-how-to-schedule-boot-time-scan-before-window-start/