Handling flexibility in an ever changing manufacturing environment is one of the key challenges for a successful industry. By using tools for virtual manufacturing, industries can analyze and predict outcomes of changes before taking action to change the real manufacturing systems. This paper describes a simulation tool that can be used to study the effect of level of automation issues on the design of manufacturing systems, including their effect on the overall system performance, ergonomics, environment, and economic measures. Determining a suitable level of automation can provide a manufacturing system with the flexibility needed to respond to the unpredictable events that occur in factory systems such as machine failures, lack of quality, lack of materials, lack of resources, etc. In addition, this tool is designed to use emerging simulation standards, allowing it to provide a neutral interface for both upstream and downstream data sources.