I have a friend that I have been taking to Mass regularly for a few months. He has even gone a few times by himself, but when we talk about him becoming Catholic, he always says, he is thinking about it, but at the same time there are things that he can not reconcile with his Protestant upbringing (Communion of Saints, Mary, Transubstantiation, Confession, you know the big stuff ;-)) What do you do in a situation like that? Is there anything that you can de besides be patient?Well, patience is key. If it was up to us, we would have everyone convert right now, this very instant. We would have them knocked down and blinded like Paul was. But, for whatever reason, God usually does not work that way. Conversion has to be the heartfelt, earnest decision of each individual or it will not be a true and lasting conversion. This conviction usually takes time to nurture and to develop.
So, patience is important, but there are a few other things you can do too.
For one, I think it's important to plug your friend into a group of good, Catholic young adults. Give him a chance to have fun and socialize with Catholics. Go out to eat, or to a movie, or a concert. Show him that Catholicism is more than the observance of rules and the upholding of certain beliefs. Show him that it's fun to be Catholic. It's cool to be Catholic. It's good to be Catholic. Catholicism is a way of life, and it's a life worth living.
Secondly, you need to bone up on your theology and your apologetics. Dust off that Bible and start reading it. He's going to have questions from time to time about why Catholics believe certain things and do what they do. You need to "always be prepared to make a defense to any one who calls you to account for the hope that is in you, yet do it with gentleness and reverence" (1 Pet 3:15). You have to take advantage of these teaching moments because they are valuable opportunities to share your faith and to bring him closer to Christ.
Finally, and perhaps most importantly, you should pray. Pray that the Lord will grant him wisdom and courage. Pray that He will soften his heart and remove all obstacles to conversion. Pray that He will grant you patience and that His Spirit will give you the right words when you don't know what to say (cf. Exo 4:10-12; Lk 12:11-12). Pray that the Lord's Will be done. Have your friends and family pray for him too.
I hope that helps.