This paper presents a contact-based micromanipulation system for the alignment and installment of microscale magnets into micro robots and devices. Affixing tweezers to a three degree of freedom micromanipulator allows for precise movement of objects. The use of non-magnetic tweezers permits the assembly of magnetized robots, and a magnetic rotating stage allows multiple magnets to be installed into one device in different orientations. By re-orienting the tweezers on the micromanipulator at defined ninety-degree angles, it is possible to assemble a device with magnets oriented in any direction on XY, XZ, and YZ planes. This system is highly precise and flexible, and can be implemented with minimal custom-made parts, making it ideal for development of new magnetic technologies at the microscale.