Modeling an effective mechanism for design and control strategies for the implementation of a flexible manufacturing system (FMS) has been a challenge. Consequently, to overcome this issue various techniques have applied in the past but most of these models are effective only for some specific situation or an element of FMS. In this study, the knowledge representation technique of Decisional DNA (DDNA) is applied to FMS to develop a generic model to achieve effective scheduling and manufacturing flexibility. Decisional DNA based Virtual Engineering Objects (VEO) are used as communicating media between machines, equipment and works pieces. The concept of Virtual Engineering Process (VEP) is applied for modeling routing flexibility. VEOs combined with VEPs form FMS-DDNA model, which facilitates in enhancing the performance of FMS, by inducing intelligence based on its own previous experience thus making it practical and smart.