I don't have time to test this, but you should be able to unlink the file before you close it. Unix will mark a file to be deleted, but it won't actually delete the file until the file is closed.
You can also open the file in read/write mode. Read from the file then truncate the file to nothing and close it.
open (FILE,"+</path/file");
flock (FILE,2);
# Do something with the data
seek (FILE,0,0);
truncate (FILE,tell (FILE));
close FILE; #file unlocks when closed
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