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With the advancement in the knowledge of surgical procedures and cell micromanipulation, there is a demand for a handheld instrument to perform micromanipulation. Hence, this paper presents a 3-DOF handheld mechanism for micromanipulation driven by three piezoelectric actuators. Flexure-based joints are utilized because of its advantages like the nonexistence of backlash and assembly errors. However, it is difficult and expensive to make such compact mechanism using traditional machining methods. In addition, the traditional machining methods are limited to simple design. To reduce the cost of fabrication and also to allow more complex designs, Objet (a rapid prototyping machine) is proposed to be used to build the mechanism. With regards to the handheld applications, the size of the mechanism is a constraint. Hence, a parallel manipulator design is the preferred choice because of its rigidity and compactness. For the illustration of an application, the mechanism is designed with an intraocular needle attached to it. Possible applications of this design include enhancement of performance in microsurgery and cell micromanipulation. Experiments are also conducted to evaluate the manipulator's tracking performance of the needle tip at a frequency of 10 Hz.