First of all you don't increment your $i

Then... What should ($final_gset[$i]), $tmps; do? I think you mean:

$final_gset[$i]= $tmps;
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don't you?

But what's the stop condition? Maybe this is, what you need:

while (<IN>) {
    if ($hit=/POLYMORPH/ ... /^\s*$/) {
        # This will be reached for each line from
        # POLIMORPH to the next empty line (including)

        # In order to exclude the first (POLYMORPH)
        # and the last (empty) line, we do
        next if $hit==1 || $hit=~/e0/i;

        # If we gut a line of data, we append them
        # to our array
        push(@final_gset, $_);

        # and get the next line
        next;
    }
    # This will be reached for anything else
}
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Your foreach-loop can be shortened to:

print TEXT join("\n",@final_gset),"\n";
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