As computer hardware advances so was the viruses that infect our PC and sometimes its very difficult to remove such viruses, in spite of the advancement of different anti-virus programs,and still end-user and even technicians end-up in reformatting one's hard drive just to get rid of particular virus(es).
It will be hard to disinfect a computer virus when it loads up at start up(and even if you start in safe mode). Trojan are the most common type of virus that infects everyone's PC worldwide(Window base OS), it(the virus) sometimes disable the functionality of some key Windows utilities(regedit,msconfig,task manager, folder options...etc) to avoid from being deleted or disabled from loading.
As PC repair technician I have deal almost all kinds of computer virus on a PC that is Window base, and often times it is a lot tedious spending time cleaning a PC infected with viruses than just reformat the whole thing and re-load the drivers and needed software.
But, their are situations that a PC has a special programs installed that the owner don't have the installer and need to be preserved, In situation such this one you have no choice but to try everything to clean the virus and have his current installation be preserved by all means.
The best way to clean an infected HDD is to pull-out the hard drive from its CPU and have it scanned by a known clean and well protected PC, normally I suggest installing at least two effective anti virus programs to have a good chance of eradicating the infection(s)of a particular hard drive, and make sure that the virus database of all your anti virus or spyware programs are up to date before inserting a hard drive that is infected with virus.
After being certain that the infection has been removed, install back the hard disk to its CPU and check if its working fine, check also if restrictions on some of the utilities mentioned above has been restored, if some of it are missing or still disabled I suggest that you download a restrictions removal tool(RRT) to solve the problem(search the net).Also don't forget to update virus pattern(s) of your anti virus and make a full scan to check if there was no more infections left.
If in any case after 2 or 3 days the same virus re-appear and mess up your PC's configuration all over again, you have no choice but to re-format the hard drive and loads a fresh copy of your OS and application softwares.
Viruses can be avoided if the user itself is cautions in dealing files coming from the net, FDD, Flash Drives, CD...etc. Plus make sure that its anti-virus pattern(virus datatbase) is always up to date and perform a regular scan at least once every week.In my experience, a lot of end-users dont care if there anti virus database is up-to-date, what most users believed that as long that they have an anti-virus program installed on their PC they are already safe.
A well informed PC user will have lower risk of a virus infection in their PC, compare to PC users that don't have proper know how in dealing computer viruses.