Not every instance of a word used in scripture means the same. It can vary with context. In the above case the word wilderness (or desert) refers to the whole of humanity (or each individual person) who is devoid of the knowledge and righteousness of God. The rest of the passage can be understood as follows:Luke 3:4-5
[4] As it is written in the book of the words of Esaias the prophet, saying, The voice of one crying in the wilderness, Prepare ye the way of the Lord, make his paths straight. [5] Every valley shall be filled, and every mountain and hill shall be brought low; and the crooked shall be made straight, and the rough ways shall be made smooth;
“Every valley shall be filled, and every mountain and hill shall be brought low;”
Way of the Lord are His commandments, which careful study prepares and diligent practice with discernment makes straight. Valley that is filled is on one hand the body which is filled with works of righteousness and on the other the soul which is filled with the knowledge of God. Mountains that are brought low are the demonic powers that set themselves against the knowledge of God (2 Cor. 10:5) and hills those that tempt us to sin. A valley is the low land that is ‘created’ between two mountains or hills, just like ignorance and evil doing are created in us by the aforementioned evil powers. The crooked ways (those related to pleasure) are made straight when the body is disciplined and brought under subjection to the spirit (1 Cor. 9:27) and the rough ways (those relating to pain) are made smooth when we embrace every trial and temptation with patience and thanksgiving.