I would suggest to look at the Bioperl HOWTO , it helped me a lot.
Here is an example code you could use to download some sequences from GenBank
and print them in multifasta output:

#!/usr/bin/perl -w

use Bio::DB::GenBank;

$db_obj = Bio::DB::GenBank->new;

    for $seq (AJ866941,DQ445088) 
    {
      $seq_obj = $db_obj->get_Seq_by_acc($seq);
      print ">",$seq_obj->display_id,"\n",
             $seq_obj->seq,"\n";
    }
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