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When it comes to scanning, you basically have two different options; Fullscan or Specified scan.
A fullscan scans the selected location, including all subfolders and all files regardless of type, size or date (except hidden and system files).

A fullscan can be started in three different ways:
  1. From the menubar

    Open the logfile and view its content

  2. By not selecting any criterias on the settings screen
    ('Scan subfolders?' needs to be checked)
  3. By rightclicking and selecting ''Run fullscan of this folder' in the treeview
A specified scan means that you select one or more criterias for the scan.
CleanMyFolder then scans the location looking for files matching your criterias.
The criterias/options for scanning is: CleanMyFolder does not scan hidden or system folders/files.
This is mostly for security reasons and to avoid possible errors.
That being said, it's not recommended to delete or move files you are unsure of.

For example:
Moving or deleting folders/files in the System32 folder, not a good idea!
CleanMyFolder Copyright © 2012 Knut Lucas Andersen.