I'm unable to mark a file

If you are unable to mark a file for removal, either by clicking its checkbox or with the Selection Assistant, this means the file is in a Protected folder.

You can tell this by the padlock shown in place of the file’s checkbox.

You can unprotect a folder tree by right-clicking the file and choosing Unprotect folder tree.

Folders are first set as protected in the Folders to search list on the Where to look tab. You can click the setting in the Protected column to change it before the scan.

Files can also be protected by a metadata filter set to Protected - change the filter and scan again to unprotect them.

Files in a virtual folder can be marked, but can’t be removed, moved or changed.