I don't know of a module that does it and didn't see one in a quick search at search.cpan.org, but it's not that hard to split them up manually.

This fragment moves a file in the current directory to a two-level subdirectory based on the first and first-and-second letters. E.g.: README.txt goes to R/RE/README.txt.

use strict;
use warnings;
use File::Spec;
use File::Path qw/mkpath/;

my $file = shift;
my $first = substr( $file, 0, 1 );
my $second = substr( $file, 0, 2 );
my $path = File::Spec->catdir( $first, $second );

mkpath( $path );
rename $file, File::Spec->catfile( $path, $file )
    or die "Can't file $file\: $!";
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