I like a girl which is in same division as I am. Recently she was suffering from malaria and when I came to know this I sent a "Get well soon!" message. We have hardly exchanged any words in labs and common lectures. Now she has replied as "thanks!" as expected. I want to give her a good reply for her thanks just to continue. So what should I say in this situation. I really like this girl!
The traditional English reply to thanks is to say "you're welcome" or various informal variants of that "it was nothing", "think nothing of it", "oh, any time", "my pleasure" and so on.
More generally, I think you need care less about that bit of the conversation. "You're welcome" suffices to reply to the thanks, but when someone has been sick, and enquiry after their well-being and expressing the hope that they are recovered should be the main part of your communiqué. But that stretches beyond questions about EL&U.
A lot of people here are suggesting something along the lines of "you're welcome" or its more casual "no problem" as a response to "thanks".
This is a very common mistake amongst non-native/L2 English speakers, as it is often learned that "thank you - you're welcome" is a standard pairing. However, there are contexts where it is not appropriate, and this is one of them.
Instead, you should say something that maintins the positive mood and attempts to keep a conversation going. You could try something like, "I hope you're feeling better" or "how are you feeling now?". These ahow that you are concerned while inviting her to reply again.
From The Kite Runner:
For you, a thousand times over.