Polydimethylsiloxane (PDMS), due to its remarkable properties such as optical transparency and ability to easily mold, is one of the most popular polymers used in micro- and nanofluidics. Furthermore, 3D printing technology due to its low cost and simplicity is also gaining a great interest among the microfluidic community. In this work, the potential of 3D printing is shown to produce microfluidic devices, their ability for studying flows and heat transfer of nanofluids, and their applicability as a heat sink device. The low-cost fused deposition modeling 3D printing technique was combined with a PDMS casting technique for the microfluidic device fabrication. The potential of this technique was experimentally demonstrated by fluid flow and heat transfer investigations using different fluids, such as distilled water-, alumina (Al2O3)-, and iron oxide (Fe3O4)-based nanofluids. The simplicity, low-cost, and unique features of the proposed heat sink device may provide a promising way to investigate nanofluids’ flow and heat transfer phenomena that are not possible to be studied by the current traditional systems.