You could drill the heads off the screws and then use some pliers to remove the remaining studs but i would only use that as a last resort.
The first thing I would try:
-Remove the master cylinder assy from the handlebar
-rest the master cylinder on a block of wood (to avoid damaging the underside of the cylinder)
-find a punch which is the same size as the head of the screws
-Give each screw a sharp tap with the punch and a hammer to force and deform the metal from the screws inward towards the middle of the screw
-Grab a phillips head screwdriver, which you will also hit sharply with a hammer into the screw
Once you have done this, don't remove the screwdriver. Try to push down into the screws and undo them. The shock from this can allow the screws to become alot easier to undo, as often corrosion is a problem here.
You only have one go at this method, and it may or may not work depending on how badly damaged the screw head is. If this does not work and the screws are badly damaged i would suggest the method of drilling out the screw heads is the only option.