Plasma-assisted Bio-extrusion System (PBS System) is an innovative hybrid bio-manufacturing system to produce complex multi-material and functionally graded scaffolds combining multiple pressure-assisted and screw-assisted printing heads and plasma jets. This approach, which represents a step forward regarding the current state of the art technology in the field of biomanufacturing, enables to design and fabricate more effective scaffolds matching the mechanical and surface characteristics of the surrounding tissue, enabling the incorporation of high number of cells uniformly distributed and the introduction of multiple cell types with positional specificity. The system requires complex control software to manipulate different materials, scaffold designs and processing parameters. This software, developed using MATLAB GUI, is detailed in this paper. It provides high freedom of design allowing the users to create single or multi-material constructs with uniform pore size or pores size gradients by changing the operation parameters, such as geometric parameters, lay-down pattern, filament distance, feed rate and layer thickness. Functionally graded scaffolds can also be designed considering different layer-by-layer coating/surface modification strategies using the multi-jet plasma system. Based on the user definition, G programming codes are generated enabling fully integration and synchronization with the hardware of the PBS system. Examples will be provided describing the design of single, multi-material and functionally graded scaffolds.