Calcium phosphate cement is a bioceramic with potential applications for bone-tissue engineering. In this work, controlled porous calcium phosphate scaffolds with interconnected pores were computationally designed by an image-based approach and fabricated by indirect solid freeform fabrication (ISFF) or ‘lost mold’ technique. Voxel finite-element analysis (FEA) showed that mechanical properties of design and fabricated scaffold can be predicted computationally. Scaffolds were then implanted subcutaneously to demonstrate tissue in-growth. Previously, we showed the ability of porous calcium phosphate cement scaffolds to have sufficiently strong mechanical properties for bone tissue engineering applications. This work shows the image-based FEAs from micro-CT scans in vivo (four- and eight weeks). Extensive new bone apposition was noted with micro-CT technique after four- and eight weeks. FEA models of the original design and scaffolds with newly bone formed were compared.