Transparency and opacity play a major role in Yevgeny Zamyatin's "We." I think transparency represents the One State because anything that is out of order can immediately be seen if everything is clear. The people live in a city made entirely of green glass, where clouds which obscure the deep blue of the sky are considered blemishes. As D-503 realized, the only thing that's not transparent is a person's body, although the eyes are still windows into the inside. When D-503 was alone with I-330 in the Ancient House he saw her in the mirror and realized that "human heads are opaque with only tiny windows in them." Although the One State could observe everybody to watch for deviant action, it couldn't see inside their heads.
Thus, the description of the man about to be executed represents a reversal of this situation. D-503 saw saw "a glass face, glass lips. And only the eyes-black, greedy, engulfing holes." The criminal's actions were revealed, and so his face and lips were glass, whereas his eyes were now not windows but deep holes, since there was nothing left for them to reveal. People like this who the One State executed represented threats to itself. However, it had scientists working on removing the threat, which they did by finding out how to remove the imagination. With the imagination gone, everything would be clear, transparent, and no deviation could occur. D-503 thought that with everyone getting the operation, "tomorrow there will be no shadows. No man, no object will cast a shadow... The sun will shine through everything."
Ironically, although the One State is transparent, its citizens have blind faith in it, and when their eyes are opened as D-503's were they see foggily. Zamyatin seems to use transparency to argue that taking away individuality takes away humanity.