Depending on the files you are trying to backup then yes it could infect a new system.
The safest way is to NOT backup any file that has as it's extension name the following
Most anything else is safe. You can try puppy linux. It will allow you to get to the files and burn them off without being in windows.
download it from HERE
and burn it to cd
if you don't have a burning program that will burn .ISO files get burncdcc from the link in my signature below. Do not burn as a data cd.
Burncdcc is a small FAST no frills iso burning program...
NOTE...do not put a blank cd in until burncdcc opens the tray for you
1. Start BurnCDCC
2. Browse to the ISO file you want to burn on cd/dvd ....in this case its puppy-2.16-seamonkey-fulldrivers.iso
3. Select the ISO file
4. click on Start
make sure in the bios the cd drive is the first boot device....
put the cd in the cd drive..boot your computer....puppy will boot and run totally in ram...if your hardware is in good working order you will know...
after you get it running and your at the desktop...you take the puppy linux cd out and then you can use the burner to copy all yor data to cd/dvds
you can also use it to backup your data to a external usb harddrive..just have it hooked to the computer when you boot up with puppy...