Because whole-computer scans take so long and make your computer so sluggish, you might schedule your computer to do its scans at a regular time when you’re not using it. Personally, I have my antivirus program scan my entire computer on Mondays at 2:00 a.m. Sometimes I stay up late on the computer on Sunday nights, but never that late. On my computer, the scan takes two or three hours, so even if I get up really early on Monday morning, the scan is usually done by the time I’m back on the computer.
You should think of a good time when your computer is always on (this is harder on laptop computers as many of us put them on “standby” or “hibernate” when we’re not using them) and schedule the scan for a time when you’re not using it. This is just my personal preference. It’s also possible that the newest and very fastest computers can better handle a full-computer virus scan while running heavyweight software such as Internet Explorer (a little sarcasm there) at the same time.