It doesn't really matter what drive Internet Explorer is on - once a virus is in your computer and running it has access to everything.
What you need to do is find a way to stop them - and Internet Explorer is the absolute worst for letting in viruses, spyware and the like.
Make sure your computer is clean of viruses and spyware by downloading and installing:
ClamWin - http://www.clamwin.com/
Spybot Search & Destroy - http://www.spybot.info/en/mirrors/index.html
Then do yourself a huge favour and stop using Internet Explorer; Firefox is a much better alternative.
Firefox - http://firefox.com/
It'll copy over your settings (cookies and favourites) from Internet Explorer, blocks pop-ups, is a lot more secure than even IE7, it's usually a lot faster... the list of awesome stuff goes on and on, but I'd like to point out the add-ons.
Please note: All add-ons are free and can usually be found on the https://addons.mozilla.org/firefox/ site... or through a Google search.
Adblock Plus will block (you guessed it) ads... banner ads, flash ads, iframe ads. It's free and can be found here:
https://addons.mozilla.org/firefox/1865/
FoxyTunes lets you control your music without having to switch to the player. It's here:
https://addons.mozilla.org/firefox/219/
There are literally more than a thousand others... feel free to look around.