By "clean", do you mean format hard drive before I install? I don't know. How does the software know it is a upgrade then?
The "software" doesn't know if it's and upgrade and doesn't care... it will easily do a clean/custom install if you can get it to boot (from cd or usb)... or you get the win 7 software DISK - which boots. What holds up the show is that the upgrade KEY CODE won't work... unless a "workaround" is used. That's why Microsoft said a "workaround" is legal.
Microsoft Says Windows 7 Install Workaround Is Legal - PC World
If your upgrade fails... or you want to upgrade from xp, or if you want to upgrade to 64 bit from 32 bit.. you must do a clean install... but then your key code won't activate windows. I suppose most people just send Microsoft some more money and get the full install key code... although they are entitled to upgrade since they paid for XP or Vista.