I am using Firefox 3.6.12, the latest version.
Although I have reported this a long time ago, CCleaner 2 and 3 still cannot clean Firefox History.
To reproduce this problem:
In Firefox, show its History "By Site".
Close Firefox and use CCleaner. Check 'Firefox/Mozilla' and 'Internet History' and clean.
Open Firefox and you will see that the History folders are there although their contents are gone. The folders have names of the sites we went to.
Hope the developers can fix this soon as it is a long standing problem.
There should be an option to just clean only the MFT instead of MFT and free space. And cleaning MFT takes too long even with one space overpass. In this regard, Eraser is faster.