Yes, you can. Our docs are not great about this but you can batch multiple FP queries in a single POST call to song/identify. The query parameter in POST mode can take a list of codes, the same one that the ENMFP and Echoprint codegens output given multiple file input. Here's an example:
caro:Geogaddi bwhitman$ cd ~/Music/iTunes/iTunes Media/Music/Boards Of Canada/Geogaddi/
caro:Geogaddi bwhitman$ ls -1 *.mp3 | ~/Downloads/ENMFP_codegen/codegen.Darwin -s 10 30 > codes.json
caro:Geogaddi bwhitman$ curl -F "api_key=XXXX" -F "query=@codes.json""http://developer.echonest.com/api/v4/song/identify"