Several important locations will be scanned in the process including running programs, browser plugins, winlogon notifications, browser helper objects, Internet Explorer toolbars or Windows Services. FreeFixer does not rate the findings which means that it is up to the user to perform further research to find out if they are dangerous or not. The software makes however use of a whitelist to remove system processes, services and other official files from the list of results to narrow down the result list to potentially dangerous ones.

Each item will be listed with its name and location, other relvant values depending on the type of item and options to lookup information about it on the Internet and to delete it.

Results can be saved in a log file for further processing. Selected items can be fixed (that means deleted) by clicking on the Fix button in the software. It is usually a good idea to perform a search on the Internet before deleting any files from the list. Some can be excluded just by looking at their names while some do not give the slightest hint at what they are.

Freefixer makes use of a database that is located on the developers website which contains additional information about each item. One interesting aspect of the database is that it will display user actions by displaying a pie chart detailing how many users kept and removed the item from their computer system.