The way profile cylinders are configured are all over the map.
The only ones you need to deal with the caps are those that use a pin to retain the plug. If that is the case you only have 2 caps to drill out, the one that tops the retainer pin, and the one that has the detent ball.
To drill these I have found that the best way is to use a sharp bit that is about 1/2 of the diameter of the cap you are drilling.
This is going to be a small bit so set your drill press speed to very fast. A drill press is recommended for this even a $50 Taiwan cheapie is better than trying to do this with a hand held.
Use a sharp punch and lightly center punch the center of the plug. If everything works as the drill breaks through the cap it will suck the cap on to the flutes of the bit.
If that doesn't happen, then drill the hole with the tap drill for a 4-40 tap and cut some threads on the inside of the hole.
Usually the tap will coax the cap off, if not then thread in a 4-40 screw and pull.
Usually this will allow you to reuse the old cap. The reason you do not want to drill out the caps over the drivers is that these are often exposed when the cylinder is installed.
Some models of profile cylinders are a bitch but with patience and practice you can key them all.
If the cylinder you have is a real cheapie the pin spacing might be off and you might need to make appropriate adjustments on the key geometry if you can.