You can make antibodies to attach to most biological molecules. The antibodies flash when lasered, the targets they are attached to can be anything. According to Cort the modern machines can simultaneously test up to (iirc) 18 different targets simultaneously. So you can make antibodies to attach to one of the CD markers on the surface, then count how many flashes you get as the blood passes through. These lasered antibodies light up these cells like lights on a Christmas tree, which then is recorded.