tux242,
What you are looking for is most likely a Hash of Hashes of Arrays (HoHoA).
Consider the following untested code:

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my @files = map { 'passwd.server' . $_ } 1 .. 9;
my %data;

for my $file (@files) {
    open (PASSWD, $file) or die "Unable to open $file : $!";
    while (<PASSWD>) {
        chomp;
        my @field = split /:/ , $_;
        $data{$file}{$field[0]} = \@field
    }
}

# Code to manipulate and identify conflicts in %data goes here
print Dumper(\%data);
[download]

I hope this helps. If I knew what sort of "clean up" you were trying to do, I would have done more.

Cheers - L~R