The focus of this dissertation is on the development of an additive manufacturing system and methodology for fabricating structures with functionally graded porous internal properties and complex three-dimensional external characteristics. For this purpose, a multi-scale three-dimensional printing system was developed, with capabilities and fabrication methodologies refined in the context of, but not limited to, manufacturing of porous bone substitutes. Porous bone implants are functionally graded structures, where internally, the design requires a gradient in porosity and mechanical properties matching the functional transition between cortical and cancellous bone regions. Geometrically, the three-dimensional shape of the design must adhere to the anatomical shape of the bone tissue being replaced. In this work, control over functionally graded porous properties was achieved by integrating specialized modules in a custom-made additive manufacturing system and studying their effect on fabricated constructs. Heterogeneous porous properties were controlled by: (i) using a micro-syringe deposition module capable of embedding sacrificial elements with a controlled feature size within the structure, (ii) controlling the amount of binder dispersed onto the powder substrate using a piezoelectric printhead, (iii) controlling the powder type or size in real-time, and/or (iv) selecting the print layer stacking orientation within the part. Characterization methods included differential scanning calorimetry (DSC)-thermo gravimetric analysis (TGA) to establish the thermal decomposition of sacrificial elements, X-ray diffraction (XRD) and dispersive X-ray spectroscopy (EDAX) to investigate the chemical composition and crystallinity, scanning electron microscopy (SEM) and optical microscopy to investigate the physical and structural properties, uniaxial mechanical loading to establish compressive strength characteristics, and porosity measurements to determine the bulk properties of the material. These studies showed that the developed system was successful in manufacturing embedded interconnected features in the range of 100-500 $ \mu m $, with a significant impact on structural properties resulting in bulk porosities in the range of 30-55% and compressive strength between 2-50 MPa. In this work, control over the the three-dimensional shape of the construct was established iteratively, by using a silhouette extraction image processing technique to determine the appropriate anisotropic compensation factors necessary to offset the effects of shrinkage in complex-shaped parts during thermal annealing. Overall shape deviations in the range of +/- 5-7 % were achieved in the second iteration for a femoral condyle implant in a sheep model. The newly developed multi-scale 3DP system and associated fabrication methodology was concluded to have great potential in manufacturing structures with functionally graded properties and complex shape characteristics.