In order better help, it would help to see a screen grab of the items you are talking about.
However, to answer your question in general terms. Any STL can be merged using the union tool and then cut using the cut tool. Note that this is much better done in CAD but it can be done albeit through a lot of trial and error in the slicer.
There may be another way to do this but this is the way I would create connectors for two STLs.
So let’s say we have two primitive shapes. A cube and a Cone. I’ll change the color so it’s easier to follow but note that color doesn’t matter.
Step 1 - Aligned the two objects to where you want them in the X-Y plane.
I’ll use the center tool to align these to objects so that I am giving the cube a dunce cap.
Step 2 - Once aligned, Shift-click the two objects you want to create dowels for and use the assembly tool to create on top level object.
Step 3 - Now that you have two objects assembled. You can manipulate the Z-axis to raise the object into position. In this example, it is the cone on top of the cube.
Step 4 - You can now merge the two objects into a single object using the “Union” tool (ver 1.7 or later of Bambu Studio)
If you change the color of one of the objects, you’ll know that the union was successful because you’ll have one color, also your assembly now only has one part.
