You've received some good suggestions from other monks so I just had a couple of comments about your code.

open (Mer, "Extracted.c");
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Always try and get in the habit of checking the return value of open:

open (MER, "Extracted.c") || 
   die "open: Extracted.c - $!\n";
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Your for looks a little out of place for processing each line in the file. I dunno, whatever floats your boat I suppose but I think you'll probably see most people use a while loop:

while (<MER>) {
   # do stuff
}
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