This isn't a problem with regular expressions. Your code only gets one line of the file at a time when you code your loop like that.

while (<Fil>) {
   #  $_ has the current line from Fil
   ...
}
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If you need to search across newline boundaries, then you should either (1) define a different boundary for each chunk to be read with $/, or (2) read the whole thing in as one big string (i.e., using no $/ at all). There are other more complicated methods, but unless we know what you're really trying to accomplish, I wouldn't go into them now.

Then when you use regular expressions, you may want to use the /s modifier as appropriate.

Details in perlvar (for $/) and perlre (for /s).