Reconstructing or repairing a damaged tissue with porous scaffolds to restore the mechanical, biological, and chemical functions is one of the major tissue engineering and wound healing strategies. Recent developments in three-dimensional bioprinting techniques and improvements in the biomaterial properties have made fabrication of controlled and interconnected porous scaffold structures possible. Especially, for wound healing or soft tissue engineering, membranes/scaffolds made out of visco-elastic hydrogels, or other soft biomaterials with regular porous structures are commonly used. When the visco-elastic structures are applied onto a wound or damaged area, various forces might act upon these structures. The applied forces caused by bandage or occlusive dressings, contraction, and/or the self-weight could deform the fabricated scaffolds. As a result, the geometry and the designed porosity changes which eventually alters the desired choreographed functionality. To remedy this problem, a denser scaffold providing higher material concentration could be developed. However, denser scaffolds might have a negative impact on cell proliferation and also could block pathways for nutrient and waste transportation. In this work, a novel multifunctional visco-elastic scaffold modeling has been proposed to control the effective porosity of scaffolds. The designed scaffolds are optimized to provide spatial functionality and controlled material concentration under deformed conditions. The proposed methodology has been implemented and illustrative examples are provided in this paper. Effective porosity between the traditional and the proposed scaffold design have been compared by applying both models on the same free-form surface mimicking a wound.