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Porous three-dimensional (3D) tissue scaffolds play an important role in cell attachment, proliferation, and guidance of new tissue formation. Performance of engineered heterogeneous tissues depends on porous scaffold microstructures with specific porosity characteristics. This paper presents our recent study on establishing topological connectivity criteria for surface matching between designed tissue scaffolds for freeform fabrication and for the insurance of suitable connections creation for scaffold flow and mass transport. To provide a structural and/or contour connectivity between surfaces, the concept of many-to-many matching of skeletal representations is adopted. The matching algorithm is based on the metric-tree encoding of surface skeletal representations, their low-distortion embeddings into normed vector spaces, and the Earth Mover's Distance under transformation.