Dear Joseph Weston,

Thanks a lot for your quick response.

I wrote a code, it is in the following: 

import kwant
import math
import matplotlib
d=1.32;
a1=2.62;
t=-0.033;
 
latt = kwant.lattice.general([(a1,0),(a1*0.5,a1*math.sqrt(3)/2)],
                                           [(a1/2,-d/2),(a1/2,d/2)])
a,b = latt.sublattices
syst= kwant.Builder()
 
def rectangle(pos):
    x, y = pos
    z=x**2+y**2
    return -3.2*a1<x<3.2*a1 and -9*d<=y<9*d 
 
syst[latt.shape(rectangle, (1,1))]=0
 
def delet(pos):
    x, y = pos
    z=x**2+y**2
    return  z<(a1)**2
 
del syst[latt.shape(delet, (1,1))] 
 
    
#nearest neighbors.............................................................
syst[[kwant.builder.HoppingKind((0,0),a,b)]] =t
syst[[kwant.builder.HoppingKind((0,1),a,b)]] =t
syst[[kwant.builder.HoppingKind((-1,1),a,b)]] =t
 
sym = kwant.TranslationalSymmetry(latt.vec((-1,0)))
    
sym.add_site_family(latt.sublattices[0], other_vectors=[(-1, 2)])
sym.add_site_family(latt.sublattices[1], other_vectors=[(-1, 2)])
lead = kwant.Builder(sym)
 
 
def lead_shape(pos):
    x, y = pos
    return   -9*d<=y<9*d and -3.2*a1<x<3.2*a1
 
lead[latt.shape(lead_shape, (1,1))] = 0
 
def delet_lead(pos):
    x, y = pos
    z=x**2+y**2
    return  z<(a1)**2
 
del lead[latt.shape(delet_lead, (1,1))]
 
 
lead[[kwant.builder.HoppingKind((0,0),a,b)]] =t
lead[[kwant.builder.HoppingKind((0,1),a,b)]] =t
lead[[kwant.builder.HoppingKind((-1,1),a,b)]] =t
 
syst.attach_lead(lead,add_cells=2)
syst.attach_lead(lead.reversed(),add_cells=2)
    
ax=kwant.plot(syst);

Making a hole on the scatter reign is ok. I did the same procedure for lead to make hole on it but at the end there isn't  any hole on the leads (it is like a rectangular). That is very kind of you if let me know what is the problem? how can I make it?

Beat wishes,
Nafise