I have an object which is going to be 3D printed to which I would like to add lot of small rivets, and to do this without losing its manifoldness. The way I've decided to do this (stupid it may be) is to place spheres in the appropriate place so that a portion of sphere is sticking out, the spheres being separate objects to the thing they are "riveting":
However, keeping them as separate objects is kinda risky (one false move...) and so I'd prefer to incorporate them into the main object. But I need to do this without destroying my manifoldness. I've tried a Boolean Union but that leaves stuff hanging over on the inside of my object, which makes it non-manifold. Is there a way to achieve my aim, or maybe an entirely different rivet strategy which I should adopt?