Shortly, the /m and /s pattern modifiers should help dealing with multi-line mathches.

       m   Treat string as multiple lines.  That is, change "^"
           and "$" from matching the start or end of the string
           to matching the start or end of any line anywhere
           within the string.

       s   Treat string as single line.  That is, change "." to
           match any character whatsoever, even a newline, which
           normally it would not match.
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Read "perldoc perlre" for more information, or post a specific problem.