I'm not even sure I should publish this because I can't really promise you that it's correct. I just wanted to take a stab at it since I couldn't find one here. From the documents I've found, M3 16mm bolts are roughly 3mm tall and 5.5mm diameter at the cap, and 16mm tall and 3mm diameter for the shaft. Do with this what you like. OpenSCAD has the ability to do boolean subtractions. You could use this to carve out an M3 bolt sized space from a model. Or not. I don't know. You're probably better off just drawing your dimensions directly into your cad file based on the dimensions listed above. Or find an official source of information about metric bolt dimensions, which I'm not.