The rationale for the use of polymer - ceramic composites for bone regeneration stems from the natural composition of bone, with collagen type I and biological apatite as main organic and inorganic constituents, respectively. In the present study, composite materials of PolyActive™ (PA), a poly (ethylene oxide terephthalate)/poly (butylene terephtalate) - (PEOT/PBT) copolymer and hydroxyapatite (HA) at a weight ratio of 85:15 were prepared by rapid prototyping (RP) using two routes. In the first approach, pre-extruded composite filaments of PA-HA were processed using three dimensional fibre deposition (3DF) (conventional composite scaffolds). In the second approach, PA scaffolds were fabricated using 3DF and combined with HA pillars that were produced inside stereolithographic moulds and that fitted inside the pores of the PA 3D structure (assembled composite scaffolds). Analysis of calcium and phosphate release in a simulated physiological solution (SPS), not containing calcium or phosphate, revealed significantly higher values for HA pillars compared to other scaffolds. Release in a simulated body fluid (SBF) that is saturated towards HA, did not show significant differences among different scaffolds. Human mesenchymal stromal cells (hMSCs) were cultured on polymer (3DF), conventional composite (3DF-HA) and assembled composite (HA assembled in 3DF) scaffolds and assessed for morphology, metabolic activity, DNA amount and gene expression of osteogenic markers using real-time quantitative PCR. SEM images showed that cells attached to and infiltrated all the scaffolds. Assembled composites had a higher metabolic activity compared to 3DF-HA scaffolds while no significant differences were observed in DNA amounts. Gene expression of osteopontin (OP) in the assembled composite was significantly higher compared to the conventional composites. The strategy of composite fabrication by assembly appears to be a promising alternative to the conventional composite fabrication route for scaffolds for bone regeneration.