How can I fetch nucleotide sequences based on ENA accession numbers and positions?
From ENA


  To retrieve results by a single identifier for all records other than
  Taxon and Project please, use the following URL syntax:
  
  http://www.ebi.ac.uk/ena/data/view/
  
  For example, the following URL returns the EMBL-Bank entry with
  accession number A00145 in HTML format:
  http://www.ebi.ac.uk/ena/data/view/A00145


Check this. 

If you use a *nix system (such as Linux, Unix, or OSX) then you can do this:

[ if list.txt contains all your ids ]

for i in `cat list.txt`; do wget -q -O $i".fa" "http://www.ebi.ac.uk/ena/data/view/"$i"&amp;display=fasta"; done


OR ELSE

Download the entire database and pick up sequences based on your identifiers, offline. You can use your favourite programming language to retrieve sequences. [I prefer awk but python is also good]