It might be a scoping issue, you didn't supply enough code for how you are feeding the list to the make_sections. Here is some code that seems to produce what you wanted if I understand correctly.

use Data::Dumper;

my @tmp;

@data = <DATA>;

make_sections(@data);

print Dumper(\@tmp);

sub make_sections {
        my $tmp;
        for (@_) {
                my $fn = $_;
                print "$fn\n";
                my $pnum = substr($fn, 6, 3);
                $pnum =~ s/0//;
                my $section = substr($fn, 5, 1);
                push @tmp, $section;
                #$MAIN::PageInfo{$section}{$pnum} = $_;
                #s/$MAIN::fileExt/$MAIN::imgExt/;
                #$MAIN::PageInfo{$section}{$fn} = $_;
                #print "Name: $PageInfo{$section}{$pnum}  Section: $se
+ction  PNum: $pnum  Thumb: $PageInfo{$section}{$fn} \n";
        }
        print "Exiting Make Sections.\n";
        return @tmp;
}

__DATA__
R3012G006.PDF
R3012G007.PDF
R3012G008.PDF
R3012H001.PDF
R3012H002.PDF
R3012H003.PDF
R3012H004.PDF
R3012H005.PDF
R3012H006.PDF
R3012J001.PDF
R3012J002.PDF
R3012J003.PDF
R3012J004.PDF
R3012J005.PDF
R3012J006.PDF
R3012J007.PDF
R3012J008.PDF
R3012J009.PDF
R3012J010.PDF
R3012J011.PDF
R3012J012.PDF
R3012J013.PDF
R3012J014.PDF
R3012J015.PDF
R3012J016.PDF
R3012J017.PDF
R3012J018.PDF
R3012J019.PDF
R3012J020.PDF
R3012J021.PDF
R3012J022.PDF
R3012J023.PDF
R3012J024.PDF
R3012J025.PDF
R3012J026.PDF
R3012J027.PDF
R3012J028.PDF
R3012J029.PDF
R3012J030.PDF
R3012J031.PDF
R3012J032.PDF
[download]

Some modifications may be needed to meet your goal, but I think it provides the results you are loooking for.