Turn off the power to the circuit prior to working on it.
Remove the existing light fixture. Test the wires with your voltage tester to ensure that the line is dead. You should see that even though it is a three-way circuit, the light fixture still gets connected to a hot and a neutral line. How the circuit was wired will determine which wires are which. For example, in some situations, a white wire may be carrying the voltage. If this is the case, it SHOULD have black tape on it, identifying it as a current-carrying line.
Assemble the ceiling fan as per the manufacturer's instructions, and hang it from a ceiling fan-rated box.
To wire the ceiling fan to the three-way switch circuit, simply connect the white fan wire to the neutral wire in the ceiling box, and connect the black and blue (if it has a light kit) wires to the hot line. Connect the ceiling fan's ground wire to the ground wire in the ceiling box. Wrap each connection with electrical tape and gently tuck the wires up into the ceiling box.
Finish installing the ceiling fan's canopy and turn the circuit back on. Your ceiling fan will now be controlled by the two three-way switches.