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backing up my computer files among many viruses

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Hi. My computer has been infected with viruses for months now. I have another staff member assisting me with that problem, but i woul like to back up my important files now before it crashes for good. This has been very close to happening several times now. I bought a 250 gig toshiba external hard drive, ( pretty nice and small) and would like to do a backup. What is the best way to go about this? It comes with a program NTI Shadow which will backup my things into a folder onto my computer. I then would have to drag that into my EHD, which would take a long time. I am more worried about storing infected files along with my own personal files. What should i do?
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