First about the GraphPad

Sorry, GraphPad Prism does not create 3-D graphs.

In this regard, we suggest you work with https://plotly.com/ online.

Dear Sandra Galea ,

I advise R software, scatterplot3d plugin. Unfortunately, it is not simple to use it.

I think for just one data plot, you can try the simple examples below:

http://www.sthda.com/english/wiki/scatterplot3d-3d-graphics-r-software-and-data-visualization

This is the complete manual about scatterplot3d in R:

https://cran.r-project.org/web/packages/scatterplot3d/vignettes/s3d.pdf

If you need further help, you can pm me.

Thank you.

You can try

JMP : https://www.jmp.com/en_sg/software/data-analysis-software.html

OR

Veusz: https://veusz.github.io