You could try using a hash to remove the duplicates or use opendir to open the directory. This is the easiest way that i could think of. Here is how you could remove the dups.

my %DupKiller;

foreach $f(@filelist){
   ###Do Your Processing Here
   $DupKiller{$f} = 1;
}

my @store = keys(%DupKiller);
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I haven't tested the code, so there might be a typo that I missed, but you can get the general idea.