You can pull the file into a 2-d array more easily:

#!/usr/bin/perl -w
use strict;            

open (FILE, $ARGV[0]) or die $!;
my @array = map {[split " "]} <FILE>;
close FILE or die $!;

for (0..$#array) {
    $array[$_][8] =~ s/%//g;
}
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The quoted space arg to split is magical, it takes care of leading and trailing whitespace too.

After Compline,
Zaxo