First, you really must "use strict" and "use warnings". There is a serious bug in your script that strict would have caught for you. The $scan in:
my $scan = 1;
is not the same as the $scan in:
if ($scan) {
The latter is actually
$main::scan, since the former is out of scope, so your script will never obey "-s".
Another problem: You don't test for success when you open MPCFG, and you open it without closing it. You could run out of open file handles, for one thing. Packages IO:File or FileHandle should be preferred for file handles; if you put them in my variables they close themselves.
Some of the other things I noticed are a matter of style. I would combine the print messages before "die" with the die command itself. You print both ordinary trace messages and errors to STDOUT. Since this is a system utility you might want better control over logging and message levels; see Log::Log4perl.
But please "use strict"!
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