We report a cost-efficient and easy to implement process for fabricating microfluidic reactors in thermoplastic materials. The method includes (i) the fabrication of an imprint template (master), which consists of a photoresist deposited on a metal plate; (ii) the thermoembossing of the reactor features into polymer sheets; (iii) the activation of the embossed and planar thermoplastic surfaces; and (iv) the low-temperature bonding of these surfaces. The generality of the method is established by fabricating microfluidic reactors with a complex geometry in a range of thermoplastic polymers, including cycloolefin, polycarbonate, and UV-transparent acrylic polymers and by the multiple, high-fidelity use of the master.