If the head has been run, the keepers get "wedged" in. The "keepers" are the 2 small pieces holding the valve in the retainer. I lightly hit the retainer with a hammer to break the keepers loose from the retainer (don't hit the top of the valve, hit the spring retainer). You can feel a difference between the valves where the keeper is stuck and those that you have broken loose as the hammer strikes feel different.
Then you should be able to put the spring removal tool on top of the spring and clamp it down. If the retainers don't come loose--carefully wiggle it and see if they do. If they still don't, you may have to try again with the hammer.
Are the heads on or off the car? If they are on the car, are you using compressed air to keep the valves closed?