It was the practice of John the Baptist to live in, and preach (call out) in the wilderness that has led us to understand Isaiah 40:3 to be a reference to John and his preaching of repentance, declaring to the people of Israel to “prepare ye a way for the Lord.” Most interpretations understand John himself to be the "voice crying in the wilderness," and that he was preparing something special for (or on behalf of) Yahweh.
Isa 40:3 The voice of him that cries in the wilderness, Prepare the way of Yahweh, make straight in the desert a highway for our God.
But, a clear understanding of Hebrew coupled with a fair reading of the Bible indicates otherwise. First of all it is not the voice that cries “in the wilderness.” It is “in the wilderness” that the "way" (or "roadway") should be prepared. Also, the roadway was to be prepared not "for our God," but "to our God."
kOl kovra` - "A cry cries!" bamid'bar panu DereC' y'hvah - “in the wilderness, turn toward a road [of] Yahweh” ya$'ru ba,araVah m'silah la`lohaynu - “make straight in a desert a course to our God.”
The ancient Hebrew people believed that mankind's contact with God was through a sort of collective conscience called chokmah (translated as "wisdom"), which called out to mankind attempting to keep him on a straight path. This conscience was thought of as "a voice calling" to mankind from out of nowhere.
Pro 1:20 Chokmah cries aloud outside; she gives her voice in the square;
Pro 8:4 I call to you, O men, and my voice is to the sons of men.
Pro 8:5 Understand chokmah, simple ones; and fools, be of an understanding heart.
Pro 3:6 In all your ways acknowledge him, and he will make your paths straight.