There is a bug in MOSS 2007 (or should I say another bug) that prevents you from deleting a copy of a .master file in Sharepoint Designer 2007.

The error message says:
This item cannot be deleted because it is still referenced by other pages

Apparently this happens because when you reset a master page to a site definition, MOSS somehow disconnects the copy file from the Sharepoint server – consequently you cannot delete it and get the “This item cannot be deleted because it is still referenced by other pages” error message.

Microsoft has this on their known issues list and suggests a workaround.
To work around this problem, mark the master file as hidden so that the master file does not appear as a selection when you create a new site.
Click here for steps

Use this as an easier workaround:

  1. Open Sharepoint Designer
  2. Create a New folder
  3. Move the ‘to be deleted’ files to this new folder
  4. Delete the folder and the files are gone… just like that !
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