split-per-3-lines

(defun split-per-3-lines (directory prefix suffix)
  (interactive
   (let (d p s)
     (setq d (read-directory-name "Directory : "))
     (setq p (read-string "prefix : "))
     (setq s (read-string "suffix : "))
     (list d p s)))
  (save-excursion
    (goto-char (point-min))
    (let ((triplets
	    (loop
	     with pre = 1
	     for i from 0
	     do (forward-line 3)
	     collect (list pre (point) i)
	     do (forward-line)
	     do (setq pre (point))
	     until (= (point) (point-max)))))
      (dolist (triplet triplets)
	(let ((s (car triplet))
	      (e (cadr triplet))
	      (i (caddr triplet)))
	  (write-region s e (format "%s/%s%06d%s.txt" directory prefix i suffix)))))))