How to remove Malware which remain in the pen drive even after Formatting!!!!!!!!!!!!

It is not safe to use pen drive even after formatting it. It still consist of viruses. Go for the solution given below:

Not on an ordinary single partitioned hard drive. Everything is wiped off so the disc is like new. 

However having said that, you saying resetting the computer to factory settings gives me the impression you have a partitioned drive with the recovery OS on it. 

When formatting a hard drive that partition would not be formatted for obvious reasons because an OS cannot delete it's self. So if you picked up a virus that targets only partitions then it would still remain on the computer. 

That's why it's always advisable to take a copy of the OS and put it on CD or DVD when you first get the computer.

In the old days when you bought a computer the OS and all the drivers came on disc. They don't do that now and put all that on a partition. If you don't take a copy [not trying to scare monger] and that drive crashes and becomes unusable you have lost the lot including your OS and drivers. If you do that copy, at least you can buy a new drive and reinstall the OS and drivers.