I'm assuming that you removed the two Allen head screws that hold the master cylinder to the 'perch' assembly .
If you have them removed, you need to a piece of hard wood, place it on the piston plunger side of the master cylinder, and give it a bit of 'persuasion' .
You've most likely have corrosion between the two parts .
Can't remember what year bike you have, it would be helpful, if you put it in your profile, as the '79-80 year bikes, came with a different reservoir than the '81 and later bikes .
There is a small hole visible from the inside of the reservoir drilled into the master cylinder body, if this becomes clogged, it will give you problems, use a soft material like a piece of copper wire to check to see if it is clear .
Like Bruce stated, there is a Phillips head screw on the bottom of the master cylinder, that holds the reservoir on, but even with the screw removed, there is an o-ring in there that can keep the reservoir from being removed .
You need to twist the reservoir back and forth to get it loose .