KiCad has “magnetic points” that can snap 2D graphics to other 2D graphics, but not to 3D models.
I would start with modifying your 3D model in some CAD program, and export it as DXF. KiCad can import DXF and you can use such a drawing directly as a PCB outline for example, by placing the graphics on the Edge.Cuts layer.
You can then also link your 3D model to a KiCad footprint, and visually inspect if the mounting holes match. Mounting holes for screws usually have a quite wide tolerance. I believe a standard hole for an M3 screw is 3.5mm, and with KiCad it’s easy to get much more precise when you zoom in.
If you know the coordinates, you can also hover over a pad and then press e for edit and directly enter coordinates.
With: Pcbnew / File / Export / Step… you can also export your project as a 3D step file, and then load it in some mechanical CAD program. You can design a housing there, or just use it to check if things fit together.