You can adapt the following to your needs (it does not cover all the ways one can put comments in code):

my $inComment = 0;
while(<>) {
  next if $inComment;
  s|//.*$||; # remove // comments
  s|/\*.*?\*/||; # remove /*..*/ comments
  s|^.*\*/|| and $inComment = 0; 
  s|/\*.*$|| and $inComment = 1; 
  # do your pattern matching on $_ here
}
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-imran