unlink join ",", @files_to_delete;

I don't think that is going to do what you expect it to do. If you have three files named a, b and c, it is literally going to try to delete a file named a,b,c. What you need is simply:

  my $nr = unlink @files_to_delete;
  if( $nr != scalar @files_to_delete ) {
     print "uh-oh: helpful error message here";
  }
[download]

I would, however, make the script run with taint checks enabled, and carefully untaint the filenames before passing them to unlink. I would also deal with each file one by one anyway:

  for( @files_to_delete ) {
     # untaint $_ here
     unlink or print "failed to remove $_: $!\n";
  }
[download]

update: looking at the OP more carefully, there are two other points to be made: firstly, you don't need to open a file in order to remove it. If you want to test that it's there you can use the -f operator. But I would just try and delete it and see what happens. Some things you can't test for, you just have to try it and see whether it works.

Secondly, unlink works in terms of the process' current directory. This might not be where you think it is. To remove the possibility of unexpected surprises, you should really be doing something like unlink "$path_to/$_" in my snippet above, where $path_to contains the name of the the directory /all/the/way/from/the/top.

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