In this paper, we demonstrate the design of a virtually alignment-free optical setup for use with microfluidic applications involving a layered glass/SU-8/PDMS (polydimethylsiloxane) chip. We show how inexpensive external lenses combined with carefully designed on-chip lenses can be used to couple light from a bulk beam to on-chip waveguides and back into a bulk beam again. Using this setup, as much as 20% of the light coming from the source can be retrieved after passing through the on-chip waveguides. The proposed setup is based on a pin-aided alignment system that makes it possible to change chips in the optical train in only a few seconds with a standard deviation of about 2% in the transmitted power. Furthermore, we demonstrate how these optical setups can be combined with microfluidics to create an on-chip flow cytometer enabling detection and counting of polystyrene particles down to 1 mm at a rate of 100 Hz.