Many viruses will be removed if you perform a FULL format. format c:/u
Even better, is to boot from a write protected startup floppy, and run fdisk.
Start with fdisk/mbr This repairs the master boot record in case it is infected.
Then, use fdisk to delete ALL logical drives and partitions.
Re-boot, run fdisk again to create the partions you desire.
This sounds more like a hardware problem to me.
My first thought is incompatible or bad memory.
I have seen RAM modules pass the POST test, but not allow Windows to load.
Next, check any plug-in cards. A bad modem or NIC are common causes of systems not booting.
In order to answer how to remove a virus from DOS mode, it helps to know the specific virus.
There are good knowledge bases with lists of virus'es, and how to remove them, at both Symantec's and McAfee's web sites.
Chas