OK, how to get what I think you're considering "3D" clouds, and often it takes not one but all three:
(1) Increase the sky's contrast in Photoshop or the equivalent software
(2) Use a polarizer when you shoot the image, to make the blue sky darker relative to the clouds
(3) Choose a day when the air has little haze and the clouds look right, and a time when the sun is in a position for the polarizer to do its job well - sometimes you must be very patient, and be willing to keep trying!
Lisa