We demonstrate the fabrication of integrated three-dimensional microchannel and optical waveguide structures inside fused silica for the interrogation and processing of single cells. The microchannels are fabricated by scanning femtosecond laser pulses (523 nm) and subsequent selective wet etching process. Optical waveguides are additionally integrated with the fabricated microchannels by scanning the laser pulse train inside the glass specimen. Single red blood cells (RBC) in diluted human blood inside of the manufactured microchannel were detected by two optical schemes. The first involved sensing the intensity change of waveguide-delivered He-Ne laser light (632.8 nm) induced by the refractive index difference of a cell flowing in the channel. The other approach was via detection of fluorescence emission from dyed RBC excited by Ar laser light (488 nm) delivered by the optical waveguide. The proposed device was tested to detect 23 fluorescent particles per second by increasing the flow rate up to 0.5 microl min(-1). The optical cell detection experiments support potential implementation of a new generation of glass-based optofluidic biochip devices in various single cell treatment processes including laser based cell processing and sensing.