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This https://netbeans.org/bugzilla/show_bug.cgi?id=200510 Fixed report pretty much describes the problem. Using build 201501250002, the refactoring window doesn't close and won't close. The window is empty and the close button is greyed out. This problem is intermittent, so the only way to reproduce is to keep refactoring. In addition, doing further refactors with an already floating window, will always use a new window. So sometimes in a single session there can be n number of these windows floating around. The only way to fix is to re-open the IDE.
Please, follow my instructions in comment #36 of the issue #200510. Thanks you. *** This bug has been marked as a duplicate of bug 200510 ***