The weapons we fight with are not the weapons of the world. On the contrary, they have divine power to demolish strongholds. 5 We demolish arguments and every pretension that sets itself up against the knowledge of God, and we take captive every thought to make it obedient to Christ.

2 Corinthians 10:4-5

We are not to merely let our thoughts happen but through the power of the Holy Spirit take every thought captive!  This means examining our thoughts and when they go against the word asking God to remove those thoughts and replace them with righteous ones.