I have written this prayer for those who are struggling with condemnation. In my experience, condemnation has a different quality than that of a guilty conscience. Condemnation tends to have a kind of incessant, beating quality to it and is not responsive to confessions or repentance. When we confess our sins God is just to forgive them (1 John 1:9). I believe the purpose of our conscience is to guide us into making choices in keeping with the will of God. When we have not done so then we need to confess our sins and repent of them in truth, that is genuinely be sorrowful for the sin itself (not that we were caught or suffered some consequence) because it displeases God. If we have done this, and made any reparation as the Holy Spirit or a spiritual counselor leads us, then our conscience should be clear.
If you are having difficulties with your conscience I would suggest first looking at scripture (in addition to commentaries if you need more clarification or further affirmation) and then seeking the advice of a spiritual counselor or elder. Many have probably committed the act you feel condemned for and so it may also be helpful to search online to see if others have sought advice on this (but all advice should be in keeping with scripture).
Prayer for Freedom from Condemnation
I have the Holy Spirit indwelling me, which has set me free from the law of sin and death and its condemnation, for there is no condemnation in those who are in Christ Jesus. Therefore, I claim that spirit of freedom that you have given me and pray that I am freed from all false condemnation, burdens or guilt. May my conscience be a faithful witness in my spirit, that my thoughts may truly and faithfully excuse me from all false guilt or burdens. Lord Jesus Christ, you are my rest and the Holy Spirit my comforter, I give unto you all of my cares and worries and pray that you take them from me, that I may rest in you and be comforted by that Holy Spirit which dwells within me.
Scripture References: Romans 8:1, Romans 2:15, Matthew 12:8, John 14:26.