You don't need File::Find. Since all your files are in the same directory, you can use a simple opendir.

my $dir = "c:/";
my @AoA = ();

#open dir and loop over files
opendir DIR, $dir or die $!;
while ( my $file = readdir(DIR) )
{
    #skip directories
    next if     -d "$dir/$file";
    #skip files that are not interesting
    next unless $file =~ /^Afj(.+)/;
    #check for existence of corresponding file    
    (warn "corresponding file not found: Cfj$1\n"), next
        unless -e "$dir/Cfj$1";
    #add to array
    push @AoA, [$file, "Cfj$1"];
}
closedir DIR;
[download]