In Matthew 7:16 we are told to that we can tell a Prophet by his fruits. If he brings good fruits he is a true prophet if he brings bad fruits he is a false prophet.  
 
Now this doesn't mean a Prophet is perfect in every action and though, since all men sin and fall short of the glory of the Lord. What it means is only a virtuous person who is working towards good not evil can be a prophet of God.  
 
In addition to this Biblical test as Latter-day Saints we always council our members and investigators to pray to Heavenly Father about these things. When we study the scriptures and pray to our Hevenly Father we can receive confimration that the Book of Mormon is true, that Josepeh Smith is the Prophet of the Restoration and that Thomas S. Monson is the living prophet.  
 
I hope my answer helps!

So you can tell he is a prophet just by the good deeds he does. That would make him a good person and maybe a good leader but that would not make him a prophet of God.

All I am doing is stating scripture, this isn't personal opinion it is strictly taken from the Holy Bible.  
 
Obviously every person that does good deeds is not a prophet, a prophet still must be called of God and ordained to that calling. The way to tell a true prophet from a false prophet though is by his fruits.

I am considering joining the church and the modern prophet topic is the one thing that is holding me back. Do you have to believe they are real prophets to join the church or could I just see them as leaders or presidents of the church?

"Do you believe the Church and gospel of Jesus Christ have been restored through the Prophet Joseph Smith? Do you believe that Thomas S. Monson is a prophet of God? What does this mean to you?" 
 
Yes, to be able to join the Church you must believe that Joseph Smith is the Prophet who Restored the Gospel to the Earth and that Thomas S. Monson the current President of the Church is the Living Prophet of God, who is called by God and ordained by the hands of the Apostles to lead the Church and receive the will of the Lord for the World.  
 
Our Church is built on the foundation of Apostles and Prophets (See Ephesians 2:20), without a Prophet and Apostles we would be in another state of Apostasy without the ability to maintain the purity of the scriptures for long.  
 
I know accepting a Living Prophet is never easy, but through study of the scriptures and much prayer you can receive the confirmation that Thomas S. Monson is a Prophet of God. I would suggest if you have the time to seek out a copy of the book To The Rescue, it is the Biography of President Monson and it contains the good fruits of his many years of service to Heavenly Father and Jesus Christ.  
 
Reading his biography might help you in this situation.

Of course I believe Joseph Smith is the prophet of the restoration.He is the one who founded the church why would I not believe he is a true prophet of God. I was talking about today's prophets like Thomas S. Monson. I'll check out that biography you spoke of.Thank you for telling me about it.

The only way one can truly know whether a man is a true prophet of God is by personal revelation through the Holy Ghost. Moroni 10:5 states that "by the power of the Holy Ghost, ye may know the truth of all things." And how does one obtain this witness? By studying it out in their minds, pondering it in their hearts and asking God in the name of Christ if it is true, believing that He will answer. We can follow this pattern for any question we may have about the gospel or just about anything, for that matter. 
However, it is not necessary to do this for every single point of doctrine. Once we have some of the basic points, such as knowing Joseph Smith was a prophet and that the Book of Mormon is true, many of the other things come simply by way of reason. 
You stated that you know that Joseph Smith was a true prophet. Knowing that, it stands to reason that the Book of Mormon must be true, for a true prophet would not, could not, produce such a book if it were not true. Likewise, if Joseph was a true prophet and the Book of Mormon is true, then the Church that Joseph Smith established must be the true Church of Jesus Christ. Those three facts stand or fall together. They are either all true or they are all false. 
When Joseph organized the Church, as part of that organization the Council of the Twelve Apostles was also reestabished on the earth. One of the main purposes of the Council of the Twelve Apostles is to ensure that the authority to lead and direct the Church remains even when the prophet passes away. The prophet and President of the Church holds all of the priesthood keys required to receive revelation for the world and to govern the affairs of the Church here on the Earth. He alone holds these keys and has the authority to excercise them. The Council of the Twelve Apostles as a body also holds these keys but they do not have the authority to excercise them unless that authority is delegated to them by the living prophet. The only exception to this is when the prophet dies. At that point, the Twelve Apostles' keys become active, allowing them to convene a solemn assembly in which they meet, pray and then, by unanimous accord, ordain the next prophet and President of the Church. And ever since the ordination of Brigham Young as the successor of Joseph Smith, the new president has always been the senior (by tenure, not age) member of the Council of the Twelve Apostles. 
Now, I go into all of this detail so that you can understand the process by which a person becomes the prophet and President of the Church, and so you can understand what it would take for someone who is NOT a true prophet to ever hold this position. In order for a FALSE prophet to become the President of the Church of Jesus Christ of Latter-day Saints, he would have to work his way up through the church ranks being called as Bishop, Stake President, Area Authority 70, etc. (note that all of these callings are given by revelation so all of the church leaders calling them to these positions would have to be fooled). Then, the current prophet and President of the Church and the Quorum of the Twelve Apostles would also have to be fooled into calling him to be a member of the 12. He would then have to somehow manage to live long enough, outliving all of the other members of the Quorum and becoming the senior Apostle. Then, at the death of the prophet, in the solemn assembly, he would have to get each of the other 11 apostles to get a false revelation from God that he was to be the next prophet. 
I hope you begin to see the impossibility of this ever happening. God set up His Church in these latter days such a way that the Church as a whole could never be led astray by His chosen prophets. In fact, were a prophet of the Church ever to begin to falter and start to go down a path where he might end up leading the Church astray, the Lord would simply and quietly bring him home. Now, are these men perfect? Of course not. Do they sometimes make mistakes? Absolutely! But can we rely on them and trust that the counsel and instruction that they give us is the mind and will of God? Again, Absolutely! 
I know that Thomas S. Monson is the current living prophet of God, just as I know that every president of the Church preceding him was also a prophet of God. Just look at the lives of these men. You will be hard pressed to find anyone on this earth who more closely followed the example of our Saviour Jesus Christ. These are not men who stood up and claimed to be prophets themselves. Rather they are righteous men who were called through revelation by righteous men who were in turn called by revelation through righteous men. Look at their lives, read their teachings, listed for the Spirit. He will testify that they are true prophets, seers and revelators.

I'm sure this has never happened in the church before but if a prophet were to tell you to do something that sounded strange or uncomfortable for you to do would you have to do it? Are you aloud to question the things he does? For that matter do you really have to even listen to him? I'm no longer talking about Thomas S. Monson I am talking about if this were to happen with a future prophet.

That is a valid and important question and that exact event has happened many times in the Church and will always happen because people have various opinions about things and many times people's opinions will conflict with the council or revelations from the Prophet.  
 
There are many examples of this, when the Prophet Joseph Smith introduced Temple Ordinances, Ordinances for the Death, Eternal Marriage,the failure of the Kirtland Savings and Trust, the persecutions of the Early Saints, ect people left the Church.  
 
It didn't end there either whenever any Prophet has received revelation or given his council to the Body of the Church some people have taken offense and at least 1 person will leave the Church.  
 
From President Woodruff's abandoning the practice of polygamy up to President Hinkley's council for women to only wear one par of modest ear rings and preferably wear no earrings or other piercings.  
 
Every time a prophet give council or receives revelation people will disagree. When such things happen one must pray to receive confirmation of the Prophets words and be humble enough to follow the will of the Lord over personal desires.  
 
Yes, it is 100% ok to question aloud anything said by any person in the Church even the prophet. A word of caution though some members will take serious offense to such things and react very unchristlike to questions against the prophet. As we are told by President Monson, we can always choose what we do but we cannot choose the consequences, of course though any harsh or unloving reactions are not appropriate and should not be taken personally.  
 
What it boils down to is no one is required to follow the Prophet's council, though not following the Prophets council can have negative effects on your standing in the Church in many instances.

I quess it is just hard for me to accept a true prophet of GOD in our time. I am going to take the advice I was given from other Mormons on how I should pray to GOD and ask if the Book Of Mormon is true before I join the church and accept modern prophets. I will not join the LDS church until he answers my prayer.