Trojan Horses Detected by WHM

We have a problem with one of our servers. It seems it has been attacked by hackers who planted a trojan virus. This affected a majority of index.html files that needed to be restored... Very frustrating!
What is the best way to get rid of the problem. Fastservers suggesting upgrading the system (for which they want to charge money)... any other solutions out there?

Thx.

 

 

 

 

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