The model of a FMS (Flexible Manufacturing System) admits to a natural hierarchical decomposition of highly decoupled units with similar structure and control. The FMS fractal architecture model represents a hierarchical structure built from elements of a single basic design. A SES (System Entity Structure) is a structural knowledge representation scheme that contains knowledge of decomposition, taxonomy, and coupling relationships of a system necessary to direct model synthesis. A substructure of a SES is extracted for use as the skeleton for a model. This substructure is called pruned SES and the extraction operation of a pruned SES from a SES is called pruning (or pruning operation). This paper presents a pruning operation called recursive pruning. It is applied to SES for generating a model structure whose sub-structure contains copies if itself as in FMS fractal architecture. Another pruning operation called delay pruning is also presented. Combined with recursive pruning the delay pruningis a useful tool for representing and constructing complex systems.