It says:

> 
> Please list up to three projects (in order of preference) you are
>  interested in.
> 
> 
> 

So I am not sure: Do I have to put in exactly three projects or can I also just put in two?
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You can put in three or fewer projects, since up to is a limiting factor, but does not require a minimum, so by this grammar, two projects would be an acceptable response.
Yes. You can put two. 

You can put one, two, or three.