Three-dimensional flow-through microchannels were fabricated inside bulk fused silica glass via ultrashort pulsed laser direct writing. The device fabrication sequence takes advantage of the nonlinear volumetric absorption in glass and the subsequent preferential chemical etching process. Optical waveguides were also written into the glass specimen and integrated with the fluidic conduits. Flow tests using both fluorescent particles and red blood cells (RBCs) were conducted on various three-dimensional channel configurations. Experiments showed the possibility for laser-induced cell processing inside the microchannels. To evaluate cytometer functionality, RBCs were detected inside the manufactured microchannel via both transmission and fluorescence probing.