The use of simulation in the design and control of manufacturing systems has become increasingly popular in the last few years. Although simulation has proven to be superior to traditional mathematical modeling in capturing the scope, complexity and dynamics of manufacturing systems, it remains merely a descriptive modeling tool. This leaves the user with the difficult tasks of generating, testing, and selecting design and operation alternatives. In this paper, a methodology that describes the supplementation of simulation systems with these more intelligent and prescriptive functions is proposed. A new architecture, based on a structured object representation (SOR) paradigm, is suggested. It is shown that the adoption of an SOR paradigm results in easier and more effective low level integration of the modeling, simulation and reasoning functions. The design of an experimental prototype system that allows automatic model generation and simulation as well as model evaluation is also presented.