Some LAPACK functions (like dgqrf) return a function where the answer is upper triangular but then there's some auxilary information stored below the diagonal. I'm wondering if there's a function that will zero out the below the diagonal entries.
General Problem
No, there is no such function in standard BLAS/LAPACK.
If you are willing to move from using BLAS/LAPACK functions directly (with all potential issues and side effects), you may find linear algebra packages that would make such operations easier. Say, Eigen would provide TriangularViews, while other packages would have their way of doing that.
If you have to use BLAS/LAPACK directly, you would have to zero out it yourself.
QR-decomposition
I assume that you don't need the Q from the QR decomposition and only care about the R. With that, you want to store it in place and clean and avoid doing a copy into another allocated storage.
Technically, you can do it using dormqr and setting matrix C to be a zero-matrix. However, it is not efficient, as you are actually performing not needed linear algebra operations and storing another dense matrix. You are certainly better off doing a manual loop to clean up if that is actually required or copy R into another place (similar to how it's done here).