I created a sort of branch system in Grasshopper (see the script joined) and I would like to have a smooth connection (see image) between the cylinder’s ends. I would like the big cylinder to be connected smoothly with the 3 branches. I am quite new to Grasshopper and Rhino and I can’t find how to do it. Any idea on how I could have a good looking result using Grasshopper or Rhino tools?
The file you posted appears to be empty.
You could cap the ends, boolean union them all together, then fillet the seams to smooth it.
Because it looks like the lower cylinder is larger than the union of the branches, you might also need to include some additional geometry in the union to connect them, such as a sphere or a cone.