A microfluidic chip requires microchannels to be created on a substrate. This paper focuses on the design and development of a precision hot embossing machine for replication of microstructures on a polymethyl methacrylate (PMMA) substrate. Kinematic coupling using three spherical balls in radial v-grooves is used to achieve precise positioning of the mold insert with the base. Flexure-based parallel guidance mechanism is used for one degree-of-freedom (DOF) motion required for the embossing process. The mechanism allows the motion of the mold normal to the substrate surface. Flexure-based kinematic coupling with the thermal center is designed to mitigate thermal stress build-up during heating and cooling of the mold insert. An Arduino-based microcontroller is developed to control the temperature profile during the process. A prototype is fabricated and experiments are performed with an aluminum mold insert on a PMMA substrate. The result shows the feasibility of the concept and the setup can be used to develop a cost-effective precision hot embossing machine for creating micropatterns for microfluidic applications.