Craniofacial prostheses are commonly used to restore aesthetics for those suffering from malformed, damaged, or missing tissue. Traditional fabrication is costly, uncomfortable for the patient, and laborious; involving several hours of hand-crafting by a prosthetist, with the results highly dependent on their skill level. In this paper, we present an advanced manufacturing framework employing three-dimensional scanning, computer-aided design, and computer-aided manufacturing to efficiently fabricate patient-specific ear prostheses. Three-dimensional scans were taken of ears of six participants using a structured light scanner. These were processed using software to model the prostheses and 3-part negative moulds, which were fabricated on a low-cost desktop 3D printer, and cast with silicone to produce ear prostheses. The average cost was approximately $3 for consumables and $116 for 2 h of labour. An injection method with smoothed 3D printed ABS moulds was also developed at a cost of approximately $155 for consumables and labour. This contrasts with traditional hand-crafted prostheses which range from $2,000 to $7,000 and take around 14 to 15 h of labour. This advanced manufacturing framework provides potential for non-invasive, low cost, and high-accuracy alternative to current techniques, is easily translatable to other prostheses, and has potential for further cost reduction.