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

You can tell this by the padlock icon next to the file name:

 

 

You can unprotect a folder tree by right-clicking on the row and selecting the 'Unprotect folder tree' command.

 

Folders are initially flagged for protection in the 'Folders to Search' list in the Scan Location tab. You can click on the button in the 'Protected' column to change the status before the scan.