Yes, you can copy your save across to another machine/the same machine after reformatting.
However, if you've plugged a USB drive into an infected computer, chances are the drive itself could have been infected too.
I would highly recommend creating an Antivirus LiveCD, booting your computer from it and checking the USB drive and saved files, before plugging the USB drive into anything else at all.
You may find you can also repair/recover your computer using the LiveCD, however if you have any questions on that, you're probably better off asking on our sister site Super User.