That seems a very clumsy way of parsing to me. You're having to re-parse the same information multiple times. And the number of times will only grow as you add more cases.

A given/when or if/elsif/.../else cascade seems far more appropriate:

#!/usr/bin/perl
use strict;
use warnings;

my $content;
my $error;

while( <DATA> ) {
    unless( s[^#include (.+)$][] ) {
        chomp;
        warn "Non-include line '$_' untouched\n";
        $content .= $_ . "\n";
    }
    else{
        local $_ = $1;
        if( m[<math] ) {
            $content .= qq[import java.lang.Math;\n];
        }
        elsif( m["stdafx.h"] ) {
            $content .= qq[#include "stdafx"\n];
        }
        elsif( m["(.+)"] ) {
            open my $inc_handle, '<', $1
                or warn "$1: $^E\n" and ++$error and next;
            local $/; # slurp
            $content .= <$inc_handle> . "\n";
        }
        else {
            warn "Unhandled include $_\n";
            $error++;
        }
    }
}
print "\nContent:\n'$content'\n";
die "$error errors encountered\n" if $error;

__DATA__
#include "stdafx.h"
#include <math.h>
#include <stdio.h>
// A comment
#include "AlyLee.h"
#include "Common.h"
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Produces:

C:\test>junk49
Unhandled include <stdio.h>
Non-include line '// A comment' untouched
AlyLee.h: The system cannot find the file specified
Common.h: The system cannot find the file specified

Content:
'#include "stdafx"
import java.lang.Math;
// A comment
'
3 errors encountered
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