Sanctification embraces the whole man, body and soul, with all the parts, members, and functions that belong to each respectively. It embraces his person and, all of his person. This is why sanctification progresses from the hour of regeneration all through life, and can be completed only in and through death.
St. Paul prays for the church of Thessalonica: "The God of peace sanctify you wholly, and may your whole spirit and soul and body be preserved blameless unto the coming of our Lord Jesus Christ." (1 Thess. v.23) Sanctification is essentially a work of one piece, simply because our person is not pieced together, but is organically one in all its parts.
The sinner's holiness or unholiness embraces his whole being. He is a sinner not only in his body, but in his soul, and even more so and in his soul not only because his will is unholy, but also because his understanding is unholy, and even more so. The memory, the imagination, and all that belongs to him as a man are radically defiled, desecrated, and corrupted by sin. He lies in the midst of death. Even in a small child, every part is affected. Without the least exertion he learns a street-song, while it seems almost impossible to commit one stanza of a psalm.
If sanctification has reference to the inherited stain, as justification to the inherited guilt, it follows that sanctification must extend as far as the inherited stain. If man's entire person is covered with the poison of the stain, it must be covered much more abundantly by sanctification.
Sin is disturbance, derangement, discord, and warfare in home and heart, and is not overcome completely until superseded by holy peace. This is the reason why St. Paul calls the God of sanctification the God of peace; and so he prays for the Church that the God of peace sanctify them wholly, or literally, "unto the full end," so that the end of sanctification may be accomplished in them perfectly. 
However, the starting-point of this grace lies not in the body, but in the soul. Sin started in the soul, not in the body; hence the mortification of sin must also begin in the soul.
It is directed, first of all, to the consciousness and to its faculties of cognition, contemplation, reflection, and judgment. Sanctification proceeds, not from the will, but from the consciousness. Sanctification is to make conformable to the will of God, and this requires, in the first place, that His good and perfect and acceptable will become a living reality to the consciousness, conviction, and conscience. The things of which one is ignorant do not affect him; but ignorance of the divine will is sin, and this must be overcome first of all.
But how? By committing to memory? By learning the Catechism? By no means. The sanctification of the consciousness consists in God's act of writing His law in our hearts. True, there are still a few traces of that law written in the sinner's heart, as the apostle writes that the Gentiles who are without the law are a law unto themselves; but this is at the most but the fermentation of a higher principle in a sinful person which can not maintain itself. The Nihilist and Communist of the day show to what extent the heart may lose the sense of the first principles of right and righteousness. But when the Scripture promises that the Lord shall write the law in their hearts, and that they shall teach no more every man his neighbor, saying, "Know the Lord, for all shall know him from the least unto the greatest," (Heb. viii.11) it offers us something entirely different and far more glorious. And this is accomplished, not by outward study, but by inward apprehension; not by an exercise of the memory, but by a renewing of the mind, as St. Paul writes: "Be not conformed to this world, but be ye transformed by the renewing of your mind, that ye may prove what is that good and acceptable and perfect will of God."
Ezekiel prophesied of this renewing of the mind when he said: "A new heart also will I give you, and a new spirit will I put within you." (Ezek. xxxvi.26) Instruction formerly received may be used as a means to that end; but the instruction which the human spirit receives in sanctification is not human, but divine. Hence it is said: "They are taught of the Lord" (Isa. liv.13); "Every man, therefore, that hath heard and learned of the Father cometh unto Me" (John vi.45); "I will put My law into their minds, and will write it in their hearts." (Jer. xxxi.33)
Since the books of Moses emphasize the fact that the tables of the law were written, not by Moses, Aholiab, nor Bezaliel, but directly by God's own finger, it follows from the nature of the case that the Scripture intends to present this writing upon the tables of the heart, not as the work of man, but as the direct work of God. The sanctification of the human consciousness is wrought in us by God in a divine, unfathomable, and irresistible way; but not independently of the Word, for that Word itself is divine, and the preaching of the Word is divinely ordained and instituted. But, since the Word and the preaching can only present the matter to the consciousness, it is the Holy Ghost who makes the heart to understand it, declares it to the consciousness, works conviction, and causes the consciousness to assent to it, and thus enables it to feel the pressure which proceeds from that which is written on the heart.
Hence the sanctification of the consciousness consists, not only in receiving new knowledge, and in being impressed with quickened conceptions, but also in having the reason qualified for the exercise of entirely different functions. For the natural man does not understand the things of the Spirit of God; but the spiritual man, i.e., he whose consciousness is regenerated, sanctified and enlightened discerns all things; for such a man, says St. Paul, has the mind of Christ.
However, the sanctification of our consciousness does not complete the sanctification of our person. On the contrary, for altho the will is absolutely dependent upon the consciousness, yet even the will itself is corrupted by sin. It did not lose its functional operation; but, as in the sinner the judgment still judges and the feeling still feels, so is the will still able to will. But its ability to reach out in every direction is lost; and the calamity has befallen us that by nature we can not will what God wills.
And that stiffness and hardness which prevent the will's free action in this respect must be removed. The Scripture calls this the taking away of the stony heart and the giving of a heart of flesh which is no longer hard and insensible. Where sin had bound the will by inclining it to evil, thereby depriving it of the power of bending in the opposite direction, i.e., toward God, the gracious gift of sanctification now comes to relieve that bending over to hell, and to give it power to incline to God.
Formerly our knowledge and conviction of the oughtness of things did not avail; for they left our will powerless as a chained wheel, unable to turn in the right direction. But not only had the consciousness a better idea of and clearer insight into the oughtness of things, and we had assented to it, but the will was also inclined by correct volition to choose the good; then the work of God had attained its end, had accomplished its purpose; and had changed the whole man.
And thus man regains also control over his passions. Every man has passions and propensities which sin has made unruly and uncontrollable. In fact, man is their toy; they can use him as they please. It is true the unconverted sometimes succeed in curbing and muzzling one passion, but always by becoming more hopelessly the slaves of another. Dissipation is conquered only by the excitement of avarice; sensuality by cherishing inward pride; anger by nursing the thirst for revenge. Kamosh is cast out only to make room for Molech; the north wind conjured away only to be followed by a blast from the east.
But the passions of the saint are controlled in a different way. Sanctification gives them another direction. He feels their whip and spur, but they are to him the violence of a foreign power. Wherefore St. Paul declares "It is no more I that do it, but sin that dwelleth in me." (Rom. vii.17, 20) And no passion can overtake him which in the power of God he can not master and control.
Sanctification embraces, in the second place, the body. Both sin and holiness affect the body not as tho it were the seat of sin, which is Manichean heresy, but in the sense in which Scripture disapproves the act of touching a corpse. The body is the instrument of the soul; hence the members may be used for holy or unholy purposes, and offer either their cooperation or resistance for such purposes. Who does not know that an excess of blood inflames the ugly temper and excites to anger; that irritable nerves make one impatient; and great muscular energy tempts to recklessness? Many are the connections between the operations of body and soul; and, inasmuch as the Holy Spirit brings the bodily members into subjection to the reign of the new life, sanctification does indeed affect the life of the body. This appears from the fact that the body is called the temple of the Holy Spirit. St. Paul calls it "the putting off of the body of sin of the flesh" (Col. ii.11); and again he saith: "Let not sin reign in your mortal body, that ye should obey the lusts thereof" (Rom. vi.12).
Hence the old man is just as bad and becomes even worse; but there is at the same time a gradual weakening -- and thus dies to his evil lusts, while the new man continues not only holy and intact, but gradually masters us and enables us to present our bodies a living sacrifice, holy and well-pleasing to God, which is our reasonable service (Rom. xii.1).
All this is wrought by the Holy Spirit who dwells in our hearts, the Comforter, Guide, and Teacher of the desolate. Christ is far from us in heaven sitting at the right hand of God. But the Holy Spirit is poured forth. He dwells in the Church on earth. Hg abides with us as our Comforter:
Hence we should not imagine that we are a full-rigged, well-provisioned craft which, at its own risk and without a pilot, swiftly carries us to the haven of rest; for without wind and tide we can not move our craft at all. The heart of the saint is a Bethel; when he rises from blessed dreams he is ever surprised to find that God is in this place and he knew it not. When we are called to speak, act, or fight, we do so as tho we were doing it all ourselves, not perceiving that it is Another who works in us both to will and to do. But as soon as we have finished the task successfully and agreeably to the will of God, as men of faith we prostrate ourselves before Him and cry, "Lord, the work was Thine."
And this goes against the old man. Before the work is undertaken he is fearful and ill at ease; but as soon as it is finished he is full of boasting, and the incense of human praise is sweet in his nostrils. But God's child works in simplicity and spontaneously, brings the sacrifice of his labor hoping against hope, with all the exertion of the talent which God gave him. But the labor finished, he wonders how he ever accomplished it, and he finds the only solution in the fact that there is One who powerfully wrought in and through him.
 This is not the place to discuss the opinion held by many, that 1 Thess. v. 23 teaches trichotomy, i.e., the threefold division of man's being. Let this only be observed, that it does not read, "Ehdpopovs," "in all your parts," followed by the summing up of those parts, spirit, soul, and body; but that it reads "O2.OTEXEGS," which refers, not to the parts, but to the final end, "TEXOS." Moreover, it should be noticed that in those passages which oppose the spiritual man to the natural--i.e., the pneumatical to the psychical, as in 1 Corinthians 2:14, 15--the word "rvevpa" indicates the new life-principle, of which it never can be said that it be preserved blameless. For this 'rvevjua " is sinless by nature. Calvin explains "spirit" and "soul" by making them to refer to our rational and moral existence as beings endowed with reason and volition, both modes of the soul's existence.