This paper presents a computer-aided design (CAD) of 3D porous tissue scaffolds with spatial control of encapsulated biomolecule distributions. A localized control of encapsulated biomolecule distribution over 3D structures is proposed to control release kinetics spatially for tissue engineering and drug release. Imaging techniques are applied to explore distribution of microspheres over porous structures. Using microspheres in this study represents a framework for modeling the distribution characteristics of encapsulated proteins, growth factors, cells, and drugs. A quantification study is then performed to assure microsphere variation over various structures under imaging analysis. The obtained distribution characteristics are mimicked by the developed stochastic modeling study of microsphere distribution over 3D engineered freeform structures. Based on the stochastic approach, 3D porous structures are modeled and designed in CAD. Modeling of microsphere and encapsulating biomaterial distribution in this work helps develop comprehensive modeling of biomolecule release kinetics for further research. A novel multichamber single nozzle solid freeform fabrication technique is utilized to fabricate sample structures. The presented methods are implemented and illustrative examples are presented in this paper.