If your set of prefixes if reasonably small, but the format and/or the variations in format make it difficult to map the sort order cleanly, then another possibility is to use a lookup table for your sorting. That way you pre-specify the order you want them in and let sort use that pre-specified order to do its work.

This isn't a very convincing demonstration, but it should serve as an illustration. It's greatest asset is its flexibility, though on large datasets it should also be pretty efficient.

#! Perl -sw
use strict;
my $index = 0;
my %lookup = map { $_ => $index++; } qw(
    CCI001
    CCI002
    CCI002A
    CCI002B
    CCI100
    CCI101
    CCI500
    CDI001
    CDJ001
);


my @data = (
    [ qw(CDJ001 1 N)],
    [ qw(CCI100 1 M)],
    [ qw(CCI001 1 M)],
    [ qw(CCI002B 1 N)],
    [ qw(CCI002 1 N)],
    [ qw(CDI001 1 M)],
    [ qw(CCI500 1 M)],
    [ qw(CCI002A 1 N)],
    [ qw(CCI101 1 N)],
);

my @sorted = sort{ $lookup{$$a[0]} <=> $lookup{$$b[0]} } @data;

print "@{$_}\n" for @sorted;
__DATA__
# Output
C:\test>196991
CCI001 1 M
CCI002 1 N
CCI002A 1 N
CCI002B 1 N
CCI100 1 M
CCI101 1 N
CCI500 1 M
CDI001 1 M
CDJ001 1 N

C:\test>
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