Rapid Prototyping (RP) techniques are commonly employed for the fabrication of structure at different scale. In this work we describe a CAD/CAM based system able to process different materials in simple or complex three-dimensional shapes. The innovation of this system is the modular approach: starting from the design of the final architecture, moving to the fabrication process and concluding with the resultant properties of the material used to fabricate a structure, it is possible to control and modulate different parameters. In the emerging approach of tissue engineering and regenerative medicine, two crucial aspects for the fabrication of a scaffold are the architecture [1] and the mechanical properties [2]. Starting from these assumptions, in this work we focus our attention on the feasibility to reproduce a biological micro-environment. Using PAM² Graphical User Interface (GUI) complex shaped geometries were designed to fabricate the desired structures. In this work we describe the control architecture of the system and show how computational models of the extrusion phase of different materials can be used to establish working parameters for the fabrication of complex micro-structures.