Thank you for your help first. I could get something useful information, even though that could not directly solve my problem.

By referring to others advice, rather than calling print_me function from .so file, I decided to call directly from C. This is what I did.

# print_me.pyx
import  numpy as np
cimport numpy as np

np.import_array()

cdef public char* print_me(f):
    cdef int[2][4] ll = [[1, 2, 3, 4], [5,6,7,8]]
    cdef np.ndarray[np.int_t, ndim=2] nll = np.zeros((4, 6), dtype=np.int)
    print nll
    nll += 1
    print nll
    return f + str(ll[1][0])

This is my .c file

// main.c
#include <python2.7/Python.h>
#include "print_me.h"

int main()
{
    // initialize python
    Py_Initialize();
    PyObject* filename = PyString_FromString("hello");
    initsquare_number();
    //initprint_me();

    // call python-oriented function
    printf("%s\n", print_me(filename));

    // finalize python
    Py_Finalize();
    return 0;
}

I compiled then as follows

# to generate print_me.c and print_me.h
cython print_me.pyx

# to build main.c and print_me.c into main.o and print_me.o
cc -c main.c print_me.c -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include

# to linke .o files
cc -lpython2.7 -ldl main.o print_me.o -o main

# execute main
./main

This results the following

[[0 0 0 0 0 0]
 [0 0 0 0 0 0]
 [0 0 0 0 0 0]
 [0 0 0 0 0 0]]
[[1 1 1 1 1 1]
 [1 1 1 1 1 1]
 [1 1 1 1 1 1]
 [1 1 1 1 1 1]]
hello5

Thank you for all of your help again!! :)