We use direct femtosecond laser writing to integrate optical waveguides into a commercial fused silica lab-on-chip (LOC). We fabricate high quality waveguides intersecting the microfluidic channels and use them to optically address with high spatial selectivity their content. Fluorescence from the photoexcited volume is efficiently collected at a 90 degrees angle by a high numerical aperture fiber, resulting in a compact and portable setup. Our approach is quite powerful because it allows the integration of photonic functionalities, by simple post-processing, into commercial LOCs, fabricated with standard techniques. By taking advantage of the unique three-dimensional capabilities of femtosecond laser writing, more complex functionalities, such as splitters or Mach-Zehnder interferometers, can be implemented.