Then be nice back. A simple thank you or I appreciate that will cover it.

If it's genuine and they sincerely believe, I think a simple thanks is appropriate.

If it's other than a kind gesture, "And I'll think for you." works well.

I say thanks to anyone who is genuinely trying to be nice. Even if it involves religious oblations.

Say “Thank you”

It’s not really a brain buster.

I tend toward awkward in those moments... I usually say, "okay..."

I nod vaguely and thank them for their positive thoughts. If it's someone I am going to keep encountering I'll say that I am not religious, but I appreciate the thought.

There's a time and place for every conversation, most of the time I say thanks and move on.

"Thank you, I'll think for you."

Christopher Hitchens

I just smile and thank them. What harm is there in that? And it makes them feel good. Kind of like petting a cat.

Thanks for your thoughts.

Thank you.

I usually just say thank you.

Smile, say ok.

It'll be a toss up between "thank you" and "oh, it's way too late for me," with a laugh.

I usually just smile. I might say, "that isn't my belief system but I'm glad you care about me" if they are saying it in a snarky way to try to play up my non belief I just ignore it because why would I have a battle of wits with an unarmed person?

I have no idea how to help you nor do I want to therefore here's some thoughts and prayers.

It depends upon how they say it to me. If they say it with a kind heart then I just smile back at them as I would if a deranged but harmless person came up to me and said something nice, possibly I would say Thanks. If it is the other version which is really a take off on 'Bless Your Heart' then I will quip something back at them because that's just my personality and my pet peeve on nasty hypocrites. I had one recently where a particularly vile woman who has caused much harm in the neighbourhood but considers herself a holy christian dropped that line on me. I told her that I thought it was nice that she had one friend in the world, even if he was only imaginary, that shut her up. It amazes me that people think they can do evil but be forgiven because they have an imaginary sky daddy watching their back.

I just say thank you. They mean well.

See... They are not trying to be nice... I have a theory, it is a fact that our brain rewards us for good behavior by shooting us up with feel good drugs, they are just dope fiends looking for a fix. They truly believe that they are helping by praying and get a small dose of the good stuff when they pray for someone right in front of them... If they were truly being altruistic then only they would know that they prayed for you. They do it more for themselves than for those whom they pray for. They may not realize it but it's true.

If they are saying it in response to a genuine problem that you are having and their only wish is to help you get through it, “I appreciate your thinking of me.” If it’s in response to something ridiculous, such as your being a non-believer, “Thank you for the thought, but I’ll rely on aids that actually exist if I need help overcoming an issue. Have a pleasant day.”

Depends on the person and the circumstances. The response can go from a simple thanks to a harsh shove it up main Street...... Something like that.....

OK is good enough but how about this one.
"You think bowing your head and closing your eyes, then talking to yourself is going to help anything?"

I usually smile , say nothing and raise my eyebrows

Curious as to how my adult Atheist son handles this I asked.
He said that he says "Please, spare me your Sorceries, I have no time for Sorcery."