An innovative rapid prototyping technique for embedding microcomponents in PDMS replicas was developed and applied on a thermal mass flowmeter for closed loop micropump flowrate control. Crucial flowmeter design and thermal parameters were investigated with a 3-D fully coupled electro-thermal-fluidic model which was built in Comsol Multiphysics 5.2. The flowmeter was characterized for three distinct measuring configurations. For precise low flowrate applications, a sensor-heater-sensor flowmeter configuration with a constant heater temperature was found to be the most appropriate yielding the measuring range of 0 to 90 µL·min⁻¹ and the sensitivity of 1.3 °C·µL⁻¹·min in the lower flowrate range of 0 to 40 µL·min⁻¹.