If we are to pray in faith, it will require our right thinking. Since our prayers are formed mainly from our soul, what we understand or believe becomes very important. This point is magnified in that our faith is directly linked to our beliefs. Believe rightly and your faith can be right. Believe wrongly and your faith will be misapplied or misused.

Second Corinthians 10:3-5 teaches us critical information about how our enemy, Satan, works to undermine our knowledge and understanding. I've included these verses from three excellent translations. As you carefully read each one, you will discover the soul (mind, emotions and will) is the arena of battle. 

King James Version:

For though we walk in the flesh, we do not war after the flesh:

4 (For the weapons of our warfare are not carnal, but mighty through God to the pulling down of strong holds;)

5 Casting down imaginations, and every high thing that exalteth itself against the knowledge of God, and bringing into captivity every thought to the obedience of Christ;  KJV

New Revised Standard Version:

Indeed, we live as human beings,[ b] but we do not wage war according to human standards;[ c]  4 for the weapons of our warfare are not merely human,[ d] but they have divine power to destroy strongholds. We destroy arguments  5 and every proud obstacle raised up against the knowledge of God, and we take every thought captive to obey Christ.  NRSV

New American Standard Bible:

For though we walk in the flesh, we do not war according to the flesh,  4 for the weapons of our warfare are not of the flesh, but [ b]divinely powerful for the destruction of fortresses.  5  We are destroying speculations and every lofty thing raised up against the knowledge of God, and  we are taking every thought captive to the obedience of Christ,  NASB

Note the use of these words in these verses. In verse four, thoughts or beliefs can be built as fortresses or strongholds used in revolt against God's Truth. Here are the most frequently used terms:

vs 4, our weapons destroy f ortresses or strongholds:

(fortresses, strongholds, wardings, strengths) Most frequent is, "strongholds."

In verse five, we destroy " arguments" that are raised up against the knowledge of God. Words that are frequently used here are:

(vain) imaginations, speculations, considerations, reasonings, arguments, deceptive fantasies, counsels. Note that these thoughts assimilate into vain imaginations, beliefs systems or ways of thinking that oppose God. These systems may become so clearly defined that they are articulated as reasonable ways of thinking about God!

If we are to pray in faith, it will require our right thinking. 

Satan also uses these vain "imaginations," to tempt us with behavior that is against the will and ways of God. Through our imagination, we can see in our mind's eye the thought scenarios we create or which are demonically dealt to us.

In the second part of verse five, we see that we can proudly identify with reasonings, or ways of thinking, just as one might identify with a theory. On the other hand, these opinions may be presented to us with undue pride. We may be made to feel foolish or stupid for believing some Biblical explanation as opposed to some popular scientific or philosophic idea.

Regarding these, Vs 5b, We destroy  proud or lofty opinions, arrogant obstacles, that are raised up against the knowledge of God.

These may be translated as: heights of man's thoughts, ideas, lofty opinions, imposing defenses erected by men, lofty thoughts, arrogant obstacles, proud obstacles, high ideas.

Don't underestimate the ability of the enemy to present these subtly, as unimportant, or as something that is not a deal-breaker of faith. The fact remains that wrong believing will not get you to right results.

What is our proper response to such attacks?

I want you to note that almost every time, the word "thoughts" is used to translate this last portion of vs five. We take captive every "thought," captive to obey Christ...

One word remains the same in almost every English translation: "thoughts."

These are the thoughts that are injected into our minds by the evil one, or thoughts which we ourselves may have contemplated.

Right thoughts are required for us to pray in faith. I have a saying I frequently use: "We think highly of the way we think." We'll attach our self-image to it and will generally defend our thoughts even in the midst of sound evidence. Not until we are overwhelmed with right information will we recant.

Furthermore, sociologists and the ad agency world has proven that if a lie is repeated often enough that we will accept it as truth. 

What thoughts are attempting to stand against God's Word in your mind? If you find yourself trying to explain away something in the Scriptures, you can be sure you have a stronghold in your soul that is working against the Spirit of God in you.

It isn't enough to pray in harmony with the will of God. We must also pray in harmony with the Truth of God if we are to effectively pray in faith!