Usual procedure is to copy files to an external storage source - e.g. CD or
similar - perhaps to your external hard drive.

Copy everything and anything you will need later (including email address book,
email messages etc - look up help for your email client to do this)

Reformat HDD and start the windows install procedure, and once that is done,
restore all datafiles back to where they came from, after reinstalling software
like your firewall and anti-virus.

Remember to update your firewall/antivirus from their respective update sites and
do a Windows Update as well.

I would then do a full virus scan of both your hdd and the external usb drive.

One more thing, if you copy files from the CD (if that is your backup method)
then you will need to reset the file attributes on all those files back to
'read/write' since copying to cd causes them to become "readonly"