The aim of this contribution is to propose the architecture for a layered design of the production system. This proposal uses the IEC 62443 norm, including the Defense-in-Depth strategy and proven technical principles applicable in a Smart Factory with a focus on communication security. Firstly, the identification of communication forms and trends in the Smart Factory environment was identified considering the spectrum of communication protocols used within various types of automation structures used in modern production facilities. The next part of the work deals with the definition of wired and wireless forms of data transfers in production systems including their advantages and disadvantages from the view of cybernetic safety and threads in communication systems, together with the description of norms from the field of security of communication systems applicable in the industrial environment. The core of this work is the proposal of the methodology to secure the Smart Factory production system in the Industry 4.0 environment. The proposal defines important implementation steps together with a summarization of the generally applicable basic principles suitable for the process of securing a Cyber production system or Smart Factory in an industrial environment, including the example of an Iptables firewall configuration within the OPC UA communication protocol and the real example of a Smart Factory production system segmentation.