Addressing EACH of the 3x3x3 LEDs separately
No, the three transistors are there to select the layer you want to control. At every moment only ONE layer can be on. But if you switch through controlling these layers fast enough, you can create the illusion of having multiple leds on even across layers. THis is because the human eyes are just not capable of seeing lights flashing at a high rate.

TL;DR
No you can't address them individually, but you can create the illusion that you can.