#!/usr/bin/perl
use strict;
use File::Find;
use Data::Dumper;

my $folder = '/folder/with/fasta/files';

my @files=();
find( \&process, $folder );
print Dumper \@files;

sub process { 
  return unless $_ =~ /CDS\.fasta$/;
  my $file = $File::Find::name;
  open my $fh,'<',$file or die $!;
  my $header = <$fh>;
  close $fh;
  push @files,[$File::Find::dir,$_,$header];
}