Prayer for your enemies is one of the deepest forms of love, because it means that you have to really want that something good happen to them.
You might do nice things for your enemy without any genuine desire that things go well with them. But prayer for them is in the presence of God who knows your heart, and prayer is interceding with God on their behalf.
It may be for their conversion. It may be for their repentance. It may be that they would be awakened to the enmity in their hearts. It may be that they will be stopped in their downward spiral of sin, even if it takes disease or calamity to do it. But the prayer Jesus has in mind here is always for their good.
This is what Jesus did as he hung on the cross:
“Father, forgive them; for they do not know what they are doing.” (Luke 23:34)
And it’s what Stephen did as he was being stoned:
Falling on his knees, he cried out with a loud voice, “Lord, do not hold this sin against them!” (Acts 7:60)
Jesus is calling us not just to do good things for our enemy, like greeting them and helping supply their needs; he is also calling us to want their best, and to express those wants in prayers when the enemy is nowhere around.
Our hearts should want their salvation and want their presence in heaven and want their eternal happiness. So we pray like the apostle Paul for the Jewish people, many of whom made life very hard for Paul,
My heart’s desire and prayer to God is for their salvation. (Romans 10:1)