Dear Hossein
                    Hexagon hole is discussed in one of the earlier post.
the way to make hexagon hole is the following

(define C->L (compose cartesian->lattice vector3))
(define (hexagon r c m)
  (list
   (make block (center c) (material m) (size (* r (sqrt 4/3)) (* 2 r)) (e1
(C->L 1 0)) (e2 (C->L 0 1)))
   (make block (center c) (material m) (size (* r (sqrt 4/3)) (* 2 r)) (e2
(C->L (/ (sqrt 3) 2) 0.5)) (e1 (C->L -0.5 (/ (sqrt 3) 2))))
   (make block (center c) (material m) (size (* r (sqrt 4/3)) (* 2 r)) (e2
(C->L (/ (sqrt 3) 2) -0.5)) (e1 (C->L 0.5 (/ (sqrt 3) 2)))) ))

using that above definition you can make hexagon with the following;
"(set! geometry ( (hexagon 12 (vector3 0 0 0) m)......"

where r is the radius of the inscribed circle r=12a,
c is the center point expressed in vector3 format
m is the material, since you want holes, make 'm' as 1.

Please check it. Bye.

with regards,
N. Yogesh
Microwave Lab,
IIT Madras, India.
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