Ultrasonic micro-molding technology can dispense, melt and inject as small an amount of polymer as is required for one cycle, an advantage which makes the process highly desirable for low-volume and customized production of micro parts made from sensitive and very expensive polymers, especially in the medical sector. In this study, the feasibility of processing the polyetheretherketone (PEEK) polymer was investigated. The experiments conducted determined the parameters of a process that would allow parts with specific mechanical properties to be produced and verified as not degraded. The development of the process used three amplitude values as well as varying plunger velocity and vibration times. The three amplitude values and four speed values were tested to determine appropriate parameters for the ultrasonic process. Completely filled samples without any visual signs of degradation were analysed using FTIR-ATR, crystallinity percentage and tensile strength tests. Results show that the amplitude parameter is an important factor in the ultrasonic process and the higher its value is, the better the mechanical properties of complete parts are. Moreover, the tensile strength value of the specimens fabricated by ultrasonic micro-molding is comparable to that of conventional injection molding technology.