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 folder name:

 

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

You will need to re-scan if you want to change the protected status of files already in the duplicate files list.

 

Note: System folders will be automatically assigned the 'Protected' status if the 'Protect important system folders' option is checkmarked in the 'Options' drop down menu.