"..to make sure he/she doesn't input the same path twice.."

Whenever you talk about _unique_ _anything_ in Perl, then it usually means that you need a hash.

my %unique_paths = ();

while (<DATA>) {
    chomp;
    my ($drive, $path) = split /:/;
    $unique_paths{$path}++;
}

for (keys %unique_paths) {
    print "$_\n";
}

__DATA__
D:/myfiles/Test/
E:/pics/cgi-bin/new/
C:/temp/
D:/new/files/
F:/new/more/
C:/test/cgi-bin/ac/
C:/new/files/
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