So you want something like this?
First, you should scale the model up by 10x or 100x to avoid creating tiny faces. Also make sure the O object is a solid group. Then make a cylinder which is also a solid object. Then you can use the Subtract from the Solid Tools to create the hole.
The way you made the other one using Intersect Faces didn’t work because you didn’t leave any of the faces from the cylinder inside the group.