It is by faith that God’s mighty power is released into the life of a Christian (Heb. 11:33-35). The fact that you have doubts indicates that you do not know God as you should. If your prayer life is infiltrated with doubts, you have denied yourself the greatest, single avenue of power that God has made available to you. Without faith it is impossible to please God (Heb. 11:6). God never comforts you in your doubt. Jesus consistently rebuked those who would not believe Him. He had revealed enough of Himself for His disciples to have believed Him in their time of need.
God wants to build your understanding of Him until your faith is sufficient to trust and obey Him in each situation (Mark 9:23-25). The moment you turn to Him with a genuine commitment to rid yourself of doubt, God will match your doubt with a revelation of Himself that can convince you of His faithfulness. When Thomas doubted, Jesus revealed Himself to him in such a way that every doubt vanished (John 20:27). You can only resolve your lack of faith in God’s presence. He must reveal Himself in such a way that any doubt you might have is removed. Jesus did this with His disciples. He involved them in a consistent, growing relationship with Himself. Jesus took them through teaching, to small miracles, to large miracles, and to the resurrection. Jesus knew that the redemption of the world rested on His disciples’ believing Him. What does God want to do in the lives of those around you that waits upon your trust in Him and the removal of your doubts?