In this research, two software packages are developed to be connected with MCNP and NJOY to obtain and extract nuclear cross sections. The first (main) software package was coupled with the MCNPX code to automatically run it to obtain cross sections of isotopes for multi-group and a wide range of incident neutron energies. It was also coupled with the second software package entitled AutoNJOY, which is directly coupled with the NJOY code, to automatically run it and obtain the cross sections of isotopes at any temperature for any reaction. The results obtained by the AutoNJOY were automatically transferred to the first software package, and the results were compared with those obtained by the MCNPX code, and the graphs of isotope cross sections were plotted in energy. The first software package is also able to analyze the microscopic cross sections obtained by the AutoNJOY and draws the graph of the cross section vs. energy. It is also able to be connected to the ACE library directly and reads microscopic cross sections of all the elements and their isotopes that have the various ZAID. It was observed that from the thermal neutron range to the fast, the cross sections of isotopes obtained by the AutoNJOY were nearly similar to the results obtained by the first software package, and the derived graphs of both methods approved with each other.