Reconstruction of craniomaxillofacial defects is a challenge for surgeons and has psychological and functional burdens for patients. Undoubtedly, there is a need for improved biomaterials and techniques for craniomaxillofacial reconstruction. We assessed the potential regeneration of bone using three modifications of a novel composite and explored the validity of a new measurement using microcomputed tomography (micro-CT). We placed three different composite samples in calvarial defects in rats and analysed healing with micro-CT. The results showed that polycaprolactone (PCL) with phosphate glass fibre is promising for non-load bearing applications in the craniomaxillofacial region. Also, the new micro-CT measurement of the temporal characterisation of the mineralisation of bone (TCBM) has the potential to evolve into a reliable predictor of bony healing and its quality.