A microfluidic chip requires micro-channels 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 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 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 micro-controller is developed to control the temperature profile during the process. A prototype is fabricated and experiments are performed with an aluminium mold insert on a PMMA substrate. The result shows the feasibility of the concept and the set-up can be used to develop a cost-effective precision hot embossing machine for creating micro-patterns for microfluidic applications.