Thanks everyone for their tips/suggestions. I've decided to approach this using a hashtable.
I came up with the following script but it doesn't seem to be working correctly.

#!/usr/bin/perl -w
$filelist = "/home/exp/acctlist.txt";
open(FILEDUPS, $filelist) || die ("Cannot open $filelist");
open($output, '>', '/home/exp/output.txt') || die ("Cannot open
file");

while ($line = <FILEDUPS>) {
chomp $line;
($filename, undef, undef, undef, undef) = split /\t/, $line;  
}

$uniquefiles{$filename} = 1;
foreach $k (keys %uniquefiles) {
print $output "$k\n";
}
[download]

It currently only outputs one line. For example, if my file contains
filename1
filename2
filename1
filename4

Then it outputs the first line only:
filename1
Where as it should output:
filename1
filename2
filename4

I've spent a long time trying to debug this, but i'm not sure where i'm going wrong.
Thanks.