Industry 4.0 represents high-level methodologies for the development of new generation manufacturing metrology systems, which are more intelligent (smart), autonomous, flexible, high-productive, and self-adaptable. One of the systems capable of responding to these challenges is a cyber-physical manufacturing metrology system (CP2MS) with techniques of artificial intelligence (AI). In general, CP2MS systems generate Big data, horizontally by integration [coordinate measuring machines (CMMs)] and vertically by control. This paper presents a cyber-physical manufacturing metrology model (CP3M) for Industry 4.0 developed by applying AI techniques such as engineering ontology (EO), ant-colony optimization (ACO), and genetic algorithms (GAs). Particularly, the CP3M presents an intelligent approach of probe configuration and setup planning for inspection of prismatic measurement parts (PMPs) on a CMM. A set of possible PMP setups and probe configurations is reduced to optimal number using developed GA-based methodology. The major novelty is the development of a new CP3M capable of responding to the requirements of an Industry 4.0 concept such as intelligent, autonomous, and productive measuring systems. As such, they respond to one smart metrology requirement within the framework of Industry 4.0, referring to the optimal number of PMPs setups and for each setup defines the configurations of probes. The main contribution of the model is productivity increase of the measuring process through the reduction of the total measurement time, as well as the elimination of errors due to the human factor through intelligent planning of probe configuration and part setup. The experiment was successfully performed using a PMP specially designed and manufactured for the purpose.