Just slurp your entire file into a single scalar (from what you describe it soulds like you're doing line-by-line processign with a while loop now). If you're processing like this now:

while(<>){
  #examine one line
}
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you can slurp the whole stream into a scalar with

my $s=join '',<>;
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and then process with a normal regular expression. Use the s flag on your regular-expression to get it to span lines.

  if($s=~/foo\s*(\d+)\s*bar/s){
...
  }
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