Monitoring of industrial cyber-physical systems (CPS) is an ongoing process necessary to ensure their security. The effectiveness of information security monitoring depends on the quality and speed of collection, processing, and analyzing of heterogeneous CPS data. Today, there are many methods of analysis for solving security problems of distributed industrial CPS. These methods have different requirements for the input data characteristics, but there are common features in them due to the subject area. The work is devoted to preliminary data processing for the security monitoring of industrial CPS in modern conditions. The general architecture defines the use of aggregation and normalization methods for data preprocessing. The work includes the issue from the requirements for the preprocessing system, the specifics of the subject area, to the general architecture and specific methods of multidimensional data aggregation.